Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/MS_1002860 Gel image file URI http://purl.obolibrary.org/obo/MS_1002845 Associated file URI URI of one gel image file associated to one PX submission. http://purl.obolibrary.org/obo/MS_1002861 Reprocessed complete dataset http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter All the raw files included in the original dataset (or group of original datasets) have been reanalysed. http://purl.obolibrary.org/obo/MS_1002855 Non peer-reviewed dataset http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter Dataset that has not been peer-reviewed by any means. http://purl.obolibrary.org/obo/MS_1002846 Associated raw file URI http://purl.obolibrary.org/obo/MS_1002845 Associated file URI URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). http://purl.obolibrary.org/obo/MS_1002853 Dataset with no associated published manuscript http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter A dataset which does not have an associated published manuscript. http://purl.obolibrary.org/obo/MS_1002867 Experimental information has been refined since this experiment was originally made publicly available http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter This means that the experimental information available has been improved, for instance precursor charges were added. http://purl.obolibrary.org/obo/MS_1002879 Progenesis QI http://purl.obolibrary.org/obo/MS_1002878 small molecule analysis software Metabolomics analysis software for LC-MS data from Nonlinear Dynamics. http://purl.obolibrary.org/obo/MS_1002984 Novor http://purl.obolibrary.org/obo/MS_1001456 analysis software Novor real-time peptide de novo sequencing software tool. http://purl.obolibrary.org/obo/MS_1003010 LPPtiger http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets. http://purl.obolibrary.org/obo/MS_1003011 pFind http://purl.obolibrary.org/obo/MS_1001456 analysis software Sequence-tag-based search engine pFind. http://purl.obolibrary.org/obo/MS_1003012 KSDP score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Kernel mass spectral dot product scoring function. http://purl.obolibrary.org/obo/MS_1003013 i3tms http://purl.obolibrary.org/obo/MS_1001456 analysis software i3-tms search engine and data-analysis software. http://purl.obolibrary.org/obo/MS_1003014 MSFragger http://purl.obolibrary.org/obo/MS_1001456 analysis software A database search-based peptide identification tool. http://purl.obolibrary.org/obo/MS_1003015 razor peptide http://purl.obolibrary.org/obo/MS_1000860 peptide Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides. http://purl.obolibrary.org/obo/MS_1003016 ProteinProphet:peptide weight http://purl.obolibrary.org/obo/MS_1002490 peptide-level scoring Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins. http://purl.obolibrary.org/obo/MS_1003017 ProteinProphet:peptide group weight http://purl.obolibrary.org/obo/MS_1002490 peptide-level scoring Fraction of peptide evidence attributable to a group of proteins. http://purl.obolibrary.org/obo/MS_1003018 Philosopher http://purl.obolibrary.org/obo/MS_1001456 analysis software General proteomics processing toolkit for shotgun proteomics. http://purl.obolibrary.org/obo/MS_1003019 pressure chromatogram http://purl.obolibrary.org/obo/MS_1000626 chromatogram type Representation of chromatographic pressure versus time. http://purl.obolibrary.org/obo/MS_1003020 flow rate chromatogram http://purl.obolibrary.org/obo/MS_1000626 chromatogram type Representation of the chromatographic flow rate versus time. http://purl.obolibrary.org/obo/MS_1003083 raw data file http://purl.obolibrary.org/obo/MS_1000577 source data file Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file). http://purl.obolibrary.org/obo/MS_1003084 processed data file http://purl.obolibrary.org/obo/MS_1000577 source data file File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument. http://purl.obolibrary.org/obo/MS_1003085 previous MSn-1 scan precursor intensity http://purl.obolibrary.org/obo/MS_1001141 intensity of precursor ion Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes. http://purl.obolibrary.org/obo/MS_1003086 precursor apex intensity http://purl.obolibrary.org/obo/MS_1001141 intensity of precursor ion Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope. http://purl.obolibrary.org/obo/MS_1003087 supported by repository but incomplete data and/or metadata http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available. http://purl.obolibrary.org/obo/MS_1003088 truncation and zlib compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Data array compression using mantissa bit truncation followed by zlib compression. http://purl.obolibrary.org/obo/MS_1003089 truncation, delta prediction and zlib compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Data array compression using mantissa bit truncation, delta prediction and zlib compression. http://purl.obolibrary.org/obo/MS_1003090 truncation, linear prediction and zlib compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Data array compression using mantissa bit truncation, linear prediction and zlib compression. http://purl.obolibrary.org/obo/MS_1003125 ProSight:spectral Q-value http://purl.obolibrary.org/obo/MS_1002354 PSM-level q-value ProSight spectrum-level Q-value. http://purl.obolibrary.org/obo/MS_1003126 ProSight:spectral P-score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic ProSight spectrum-level P-score. http://purl.obolibrary.org/obo/MS_1003128 ProSight:spectral C-score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic ProSight spectrum-level C-score. http://purl.obolibrary.org/obo/MS_1003129 proteoform-level Q-value http://purl.obolibrary.org/obo/MS_1002905 proteoform-level identification statistic Estimation of the Q-value for proteoforms. http://purl.obolibrary.org/obo/MS_1003130 ProSight:proteoform Q-value http://purl.obolibrary.org/obo/MS_1003129 proteoform-level Q-value ProSight proteoform-level Q-value. http://purl.obolibrary.org/obo/MS_1003131 isoform-level identification attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Isoform level information. http://purl.obolibrary.org/obo/MS_1003451 FAIMS compensation voltage ramp end http://purl.obolibrary.org/obo/MS_1003254 peak attribute DC potential at the end of the FAIMS voltage ramp. http://purl.obolibrary.org/obo/MS_1000001 sample number http://purl.obolibrary.org/obo/MS_1000548 sample attribute A reference number relevant to the sample under study. http://purl.obolibrary.org/obo/MS_1000002 sample name http://purl.obolibrary.org/obo/MS_1000548 sample attribute A reference string relevant to the sample under study. http://purl.obolibrary.org/obo/MS_1000003 sample state http://purl.obolibrary.org/obo/MS_1000548 sample attribute The chemical phase of a pure sample, or the state of a mixed sample. http://purl.obolibrary.org/obo/MS_1000004 sample mass http://purl.obolibrary.org/obo/MS_1000548 sample attribute Total mass of sample used. http://purl.obolibrary.org/obo/MS_1000005 sample volume http://purl.obolibrary.org/obo/MS_1000548 sample attribute Total volume of solution used. http://purl.obolibrary.org/obo/MS_1000006 sample concentration http://purl.obolibrary.org/obo/MS_1000548 sample attribute Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used. http://purl.obolibrary.org/obo/MS_1000011 mass resolution http://purl.obolibrary.org/obo/MS_1000503 scan attribute Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height. http://purl.obolibrary.org/obo/MS_1000012 resolution measurement method http://purl.obolibrary.org/obo/MS_1000596 measurement method Which of the available standard measures is used to define whether two peaks are separate. http://purl.obolibrary.org/obo/MS_1000014 accuracy http://purl.obolibrary.org/obo/MS_1000480 mass analyzer attribute Accuracy is the degree of conformity of a measured mass to its actual value. http://purl.obolibrary.org/obo/MS_1000015 scan rate http://purl.obolibrary.org/obo/MS_1000503 scan attribute Rate in Th/sec for scanning analyzers. http://purl.obolibrary.org/obo/MS_1000016 scan start time http://purl.obolibrary.org/obo/MS_1002345 PSM-level attribute The time that an analyzer started a scan, relative to the start of the MS run. http://purl.obolibrary.org/obo/MS_1000021 reflectron state http://purl.obolibrary.org/obo/MS_1000480 mass analyzer attribute Status of the reflectron, turned on or off. http://purl.obolibrary.org/obo/MS_1000022 TOF Total Path Length http://purl.obolibrary.org/obo/MS_1000480 mass analyzer attribute The length of the field free drift space in a time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1000024 final MS exponent http://purl.obolibrary.org/obo/MS_1000480 mass analyzer attribute Final MS level achieved when performing PFF with the ion trap (e.g. MS E10). http://purl.obolibrary.org/obo/MS_1000025 magnetic field strength http://purl.obolibrary.org/obo/MS_1000480 mass analyzer attribute A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity. http://purl.obolibrary.org/obo/MS_1000028 detector resolution http://purl.obolibrary.org/obo/MS_1000481 detector attribute The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height. http://purl.obolibrary.org/obo/MS_1000029 sampling frequency http://purl.obolibrary.org/obo/MS_1000481 detector attribute The rate of signal sampling (measurement) with respect to time. http://purl.obolibrary.org/obo/MS_1000032 customization http://purl.obolibrary.org/obo/MS_1000496 instrument attribute Free text description of a single customization made to the instrument; for several modifications, use several entries. http://purl.obolibrary.org/obo/MS_1000033 deisotoping http://purl.obolibrary.org/obo/MS_1000543 data processing action The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution. http://purl.obolibrary.org/obo/MS_1000034 charge deconvolution http://purl.obolibrary.org/obo/MS_1000543 data processing action The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions. http://purl.obolibrary.org/obo/MS_1000035 peak picking http://purl.obolibrary.org/obo/MS_1000543 data processing action Spectral peak processing conducted on the acquired data to convert profile data to centroided data. http://purl.obolibrary.org/obo/MS_1000040 m/z http://purl.obolibrary.org/obo/UO_0000000 unit Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated. http://purl.obolibrary.org/obo/MS_1000041 charge state http://purl.obolibrary.org/obo/MS_1000507 ion property Number of net charges, positive or negative, on an ion. http://purl.obolibrary.org/obo/MS_1000042 peak intensity http://purl.obolibrary.org/obo/MS_1000455 ion selection attribute Intensity of ions as measured by the height or area of a peak in a mass spectrum. http://purl.obolibrary.org/obo/MS_1000043 intensity unit http://purl.obolibrary.org/obo/UO_0000000 unit Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors. http://purl.obolibrary.org/obo/MS_1000045 collision energy http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion. http://purl.obolibrary.org/obo/MS_1000046 energy unit http://purl.obolibrary.org/obo/UO_0000000 unit OBSOLETE Energy units are represented in either eV or Joules. http://purl.obolibrary.org/obo/MS_1000047 emulsion http://purl.obolibrary.org/obo/MS_1000003 sample state State if the sample is in emulsion form. http://purl.obolibrary.org/obo/MS_1000048 gaseous sample state http://purl.obolibrary.org/obo/MS_1000003 sample state State if the sample is in gaseous form. http://purl.obolibrary.org/obo/MS_1000049 liquid sample state http://purl.obolibrary.org/obo/MS_1000003 sample state State if the sample is in liquid form. http://purl.obolibrary.org/obo/MS_1000050 solid sample state http://purl.obolibrary.org/obo/MS_1000003 sample state State if the sample is in solid form. http://purl.obolibrary.org/obo/MS_1000051 solution http://purl.obolibrary.org/obo/MS_1000003 sample state State if the sample is in solution form. http://purl.obolibrary.org/obo/MS_1000052 suspension http://purl.obolibrary.org/obo/MS_1000003 sample state State if the sample is in suspension form. http://purl.obolibrary.org/obo/MS_1000053 sample batch http://purl.obolibrary.org/obo/MS_1000548 sample attribute Sample batch lot identifier. http://purl.obolibrary.org/obo/MS_1000055 continuous flow fast atom bombardment http://purl.obolibrary.org/obo/MS_1000007 inlet type Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix. http://purl.obolibrary.org/obo/MS_1000056 direct inlet http://purl.obolibrary.org/obo/MS_1000007 inlet type The sample is directly inserted into the ion source, usually on the end of a heatable probe. http://purl.obolibrary.org/obo/MS_1000057 electrospray inlet http://purl.obolibrary.org/obo/MS_1000007 inlet type Inlet used for introducing the liquid sample into an electrospray ionization source. http://purl.obolibrary.org/obo/MS_1000058 flow injection analysis http://purl.obolibrary.org/obo/MS_1000007 inlet type A sample introduction method in which a discrete sample aliquot is injected into a continuous carrier solvent stream and transported to the ionization source without separation, producing a transient analytical signal. http://purl.obolibrary.org/obo/MS_1000059 inductively coupled plasma http://purl.obolibrary.org/obo/MS_1000007 inlet type A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction. http://purl.obolibrary.org/obo/MS_1000060 infusion http://purl.obolibrary.org/obo/MS_1000007 inlet type A sample introduction method in which a sample solution is continuously delivered to the ionization source at a constant flow rate without separation. http://purl.obolibrary.org/obo/MS_1000061 jet separator http://purl.obolibrary.org/obo/MS_1000007 inlet type A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity. http://purl.obolibrary.org/obo/MS_1000062 membrane separator http://purl.obolibrary.org/obo/MS_1000007 inlet type A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane. http://purl.obolibrary.org/obo/MS_1000063 moving belt http://purl.obolibrary.org/obo/MS_1000007 inlet type Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules. http://purl.obolibrary.org/obo/MS_1000064 moving wire http://purl.obolibrary.org/obo/MS_1000007 inlet type Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules. http://purl.obolibrary.org/obo/MS_1000065 open split http://purl.obolibrary.org/obo/MS_1000007 inlet type A division of flowing stream of liquid into two streams. http://purl.obolibrary.org/obo/MS_1000066 particle beam http://purl.obolibrary.org/obo/MS_1000007 inlet type Method for generating ions from a solution of an analyte. http://purl.obolibrary.org/obo/MS_1000067 reservoir http://purl.obolibrary.org/obo/MS_1000007 inlet type A sample inlet method involving a reservoir. http://purl.obolibrary.org/obo/MS_1000068 septum http://purl.obolibrary.org/obo/MS_1000007 inlet type A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber. http://purl.obolibrary.org/obo/MS_1000069 thermospray inlet http://purl.obolibrary.org/obo/MS_1000007 inlet type A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample. http://purl.obolibrary.org/obo/MS_1000070 atmospheric pressure chemical ionization http://purl.obolibrary.org/obo/MS_1000240 atmospheric pressure ionization Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization. http://purl.obolibrary.org/obo/MS_1000071 chemical ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization. http://purl.obolibrary.org/obo/MS_1000074 fast atom bombardment ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization. http://purl.obolibrary.org/obo/MS_1000075 matrix-assisted laser desorption ionization http://purl.obolibrary.org/obo/MS_1000247 desorption ionization The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization. http://purl.obolibrary.org/obo/MS_1000076 negative polarity acquisition http://purl.obolibrary.org/obo/MS_1003776 acquisition polarity Polarities of the scans of a run are all negative. http://purl.obolibrary.org/obo/MS_1000077 positive polarity acquisition http://purl.obolibrary.org/obo/MS_1003776 acquisition polarity Polarities of the scans of a run are all positive. http://purl.obolibrary.org/obo/MS_1000078 axial ejection linear ion trap http://purl.obolibrary.org/obo/MS_1000291 linear ion trap A linear ion trap mass analyzer where ions are ejected along the axis of the analyzer. http://purl.obolibrary.org/obo/MS_1000079 fourier transform ion cyclotron resonance http://purl.obolibrary.org/obo/MS_1000443 mass analyzer type A device based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z. http://purl.obolibrary.org/obo/MS_1000080 magnetic sector http://purl.obolibrary.org/obo/MS_1000443 mass analyzer type A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z. http://purl.obolibrary.org/obo/MS_1000081 quadrupole http://purl.obolibrary.org/obo/MS_1000443 mass analyzer type A device that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. http://purl.obolibrary.org/obo/MS_1000082 quadrupole ion trap http://purl.obolibrary.org/obo/MS_1000264 ion trap Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials. http://purl.obolibrary.org/obo/MS_1000083 radial ejection linear ion trap http://purl.obolibrary.org/obo/MS_1000291 linear ion trap A linear ion trap mass analyzer where ions are ejected along the radius of the analyzer. http://purl.obolibrary.org/obo/MS_1000084 time-of-flight http://purl.obolibrary.org/obo/MS_1000443 mass analyzer type Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy. http://purl.obolibrary.org/obo/MS_1000085 baseline http://purl.obolibrary.org/obo/MS_1000012 resolution measurement method An attribute of resolution when recording the detector response in absence of the analyte. http://purl.obolibrary.org/obo/MS_1000086 full width at half-maximum http://purl.obolibrary.org/obo/MS_1000012 resolution measurement method A measure of resolution represented as width of the peak at half peak height. http://purl.obolibrary.org/obo/MS_1000087 ten percent valley http://purl.obolibrary.org/obo/MS_1000012 resolution measurement method An attribute of resolution when the ratio between adjacent signals is 10% of the signal height. http://purl.obolibrary.org/obo/MS_1000092 decreasing m/z scan http://purl.obolibrary.org/obo/MS_1000018 scan direction High to low direction in terms of m/z of the scan for scanning analyzers. http://purl.obolibrary.org/obo/MS_1000093 increasing m/z scan http://purl.obolibrary.org/obo/MS_1000018 scan direction Low to high direction in terms of m/z of the scan for scanning analyzers. http://purl.obolibrary.org/obo/MS_1000094 exponential http://purl.obolibrary.org/obo/MS_1000019 scan law The mass scan is done in exponential mode. http://purl.obolibrary.org/obo/MS_1000095 linear http://purl.obolibrary.org/obo/MS_1000019 scan law OBSOLETE The mass scan is done in linear mode. http://purl.obolibrary.org/obo/MS_1000096 quadratic http://purl.obolibrary.org/obo/MS_1000019 scan law The mass scan is done in quadratic mode. http://purl.obolibrary.org/obo/MS_1000105 reflectron off http://purl.obolibrary.org/obo/MS_1000021 reflectron state Reflectron is off. http://purl.obolibrary.org/obo/MS_1000106 reflectron on http://purl.obolibrary.org/obo/MS_1000021 reflectron state Reflectron is on. http://purl.obolibrary.org/obo/MS_1000107 channeltron http://purl.obolibrary.org/obo/MS_1000026 detector type A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse. http://purl.obolibrary.org/obo/MS_1000108 conversion dynode electron multiplier http://purl.obolibrary.org/obo/MS_1000346 conversion dynode A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected. http://purl.obolibrary.org/obo/MS_1000109 conversion dynode photomultiplier http://purl.obolibrary.org/obo/MS_1000346 conversion dynode A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier. http://purl.obolibrary.org/obo/MS_1000110 daly detector http://purl.obolibrary.org/obo/MS_1000026 detector type Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector. http://purl.obolibrary.org/obo/MS_1000111 electron multiplier tube http://purl.obolibrary.org/obo/MS_1000253 electron multiplier A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. http://purl.obolibrary.org/obo/MS_1000112 faraday cup http://purl.obolibrary.org/obo/MS_1000026 detector type A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device. http://purl.obolibrary.org/obo/MS_1000113 focal plane array http://purl.obolibrary.org/obo/MS_1000348 focal plane collector An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. http://purl.obolibrary.org/obo/MS_1000114 microchannel plate detector http://purl.obolibrary.org/obo/MS_1000345 array detector A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate. http://purl.obolibrary.org/obo/MS_1000115 multi-collector http://purl.obolibrary.org/obo/MS_1000026 detector type A detector system commonly used in inductively coupled plasma mass spectrometers. http://purl.obolibrary.org/obo/MS_1000116 photomultiplier http://purl.obolibrary.org/obo/MS_1000026 detector type A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected. http://purl.obolibrary.org/obo/MS_1000117 analog-digital converter http://purl.obolibrary.org/obo/MS_1000027 detector acquisition mode Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers. http://purl.obolibrary.org/obo/MS_1000118 pulse counting http://purl.obolibrary.org/obo/MS_1000027 detector acquisition mode Definition to do. http://purl.obolibrary.org/obo/MS_1000119 time-digital converter http://purl.obolibrary.org/obo/MS_1000027 detector acquisition mode A device for converting a signal of sporadic pluses into a digital representation of their time indices. http://purl.obolibrary.org/obo/MS_1000120 transient recorder http://purl.obolibrary.org/obo/MS_1000027 detector acquisition mode A detector acquisition mode used for detecting transient signals. http://purl.obolibrary.org/obo/MS_1000121 SCIEX instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model SCIEX instrument model. http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Bruker Daltonics' instrument model. http://purl.obolibrary.org/obo/MS_1000123 IonSpec instrument model http://purl.obolibrary.org/obo/MS_1000489 Varian instrument model IonSpec corporation instrument model. http://purl.obolibrary.org/obo/MS_1000124 Shimadzu instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Shimadzu corporation instrument model. http://purl.obolibrary.org/obo/MS_1000125 Thermo Finnigan instrument model http://purl.obolibrary.org/obo/MS_1000483 Thermo Fisher Scientific instrument model ThermoFinnigan from Thermo Electron Corporation instrument model. http://purl.obolibrary.org/obo/MS_1000126 Waters instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Waters Corporation instrument model. http://purl.obolibrary.org/obo/MS_1000127 centroid spectrum http://purl.obolibrary.org/obo/MS_1000525 spectrum representation Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset. http://purl.obolibrary.org/obo/MS_1000128 profile spectrum http://purl.obolibrary.org/obo/MS_1000525 spectrum representation A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. http://purl.obolibrary.org/obo/MS_1000129 negative scan http://purl.obolibrary.org/obo/MS_1000808 chromatogram attribute Polarity of the scan is negative. http://purl.obolibrary.org/obo/MS_1000130 positive scan http://purl.obolibrary.org/obo/MS_1000808 chromatogram attribute Polarity of the scan is positive. http://purl.obolibrary.org/obo/MS_1000131 number of detector counts http://purl.obolibrary.org/obo/MS_1000043 intensity unit The number of counted events observed in one or a group of elements of a detector. http://purl.obolibrary.org/obo/MS_1000132 percent of base peak http://purl.obolibrary.org/obo/MS_1000043 intensity unit The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity. http://purl.obolibrary.org/obo/MS_1000133 collision-induced dissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended. http://purl.obolibrary.org/obo/MS_1000134 plasma desorption http://purl.obolibrary.org/obo/MS_1000044 dissociation method The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. http://purl.obolibrary.org/obo/MS_1000135 post-source decay http://purl.obolibrary.org/obo/MS_1000044 dissociation method A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra. http://purl.obolibrary.org/obo/MS_1000136 surface-induced dissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method Fragmentation that results from the collision of an ion with a surface. http://purl.obolibrary.org/obo/MS_1000138 normalized collision energy http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions. http://purl.obolibrary.org/obo/MS_1000139 4000 QTRAP http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument Applied Biosystems/MDS SCIEX Q 4000 TRAP MS. http://purl.obolibrary.org/obo/MS_1000140 4700 Proteomics Analyzer http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS. http://purl.obolibrary.org/obo/MS_1000141 apex IV http://purl.obolibrary.org/obo/MS_1003948 fourier transform ion cyclotron resonance instrument Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. http://purl.obolibrary.org/obo/MS_1000142 apex Q http://purl.obolibrary.org/obo/MS_1003766 quadrupole fourier transform ion cyclotron resonance instrument Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. http://purl.obolibrary.org/obo/MS_1000143 API 150EX http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Applied Biosystems/MDS SCIEX API 150EX MS. http://purl.obolibrary.org/obo/MS_1000144 API 150EX Prep http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Applied Biosystems/MDS SCIEX API 150EX Prep MS. http://purl.obolibrary.org/obo/MS_1000145 API 2000 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Applied Biosystems/MDS SCIEX API 2000 MS. http://purl.obolibrary.org/obo/MS_1000146 API 3000 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Applied Biosystems/MDS SCIEX API 3000 MS. http://purl.obolibrary.org/obo/MS_1000147 API 4000 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Applied Biosystems/MDS SCIEX API 4000 MS. http://purl.obolibrary.org/obo/MS_1000148 autoflex II http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' autoflex II: MALDI TOF. http://purl.obolibrary.org/obo/MS_1000149 autoflex TOF/TOF http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF. http://purl.obolibrary.org/obo/MS_1000150 Auto Spec Ultima NT http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Waters magnetic sector based AutoSpec Ultima NT MS. http://purl.obolibrary.org/obo/MS_1000151 BioTOF II http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' BioTOF II: ESI TOF. http://purl.obolibrary.org/obo/MS_1000152 BioTOF-Q http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' BioTOF-Q: ESI Q-TOF. http://purl.obolibrary.org/obo/MS_1000153 DELTA plusAdvantage http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument ThermoFinnigan DELTA plusAdvantage MS. http://purl.obolibrary.org/obo/MS_1000154 DELTAplusXP http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument ThermoFinnigan DELTAplusXP MS. http://purl.obolibrary.org/obo/MS_1000156 esquire 4000 http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1000157 esquire 6000 http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1000158 explorer http://purl.obolibrary.org/obo/MS_1003948 fourier transform ion cyclotron resonance instrument IonSpec Explorer MS. http://purl.obolibrary.org/obo/MS_1000159 GCT http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Waters oa-ToF based GCT. http://purl.obolibrary.org/obo/MS_1000160 HCT http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1000161 HCTplus http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1000162 HiRes ESI http://purl.obolibrary.org/obo/MS_1003948 fourier transform ion cyclotron resonance instrument IonSpec HiResESI MS. http://purl.obolibrary.org/obo/MS_1000163 HiRes MALDI http://purl.obolibrary.org/obo/MS_1003948 fourier transform ion cyclotron resonance instrument IonSpec HiResMALDI MS. http://purl.obolibrary.org/obo/MS_1000164 IsoPrime http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Waters IsoPrime MS. http://purl.obolibrary.org/obo/MS_1000165 IsoProbe http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Waters IsoProbe MS. http://purl.obolibrary.org/obo/MS_1000166 IsoProbe T http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Waters IsoProbe T MS. http://purl.obolibrary.org/obo/MS_1000167 LCQ Advantage http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument ThermoFinnigan LCQ Advantage MS. http://purl.obolibrary.org/obo/MS_1000168 LCQ Classic http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument ThermoFinnigan LCQ Classic MS. http://purl.obolibrary.org/obo/MS_1000169 LCQ Deca XP Plus http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument ThermoFinnigan LCQ Deca XP Plus MS. http://purl.obolibrary.org/obo/MS_1000170 M@LDI L http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Waters oa-ToF based MALDI L. http://purl.obolibrary.org/obo/MS_1000171 M@LDI LR http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Waters oa-ToF based MALDI LR. http://purl.obolibrary.org/obo/MS_1000172 MAT253 http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument ThermoFinnigan MAT253 MS. http://purl.obolibrary.org/obo/MS_1000173 MAT900XP http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument ThermoFinnigan MAT900XP MS. http://purl.obolibrary.org/obo/MS_1000174 MAT900XP Trap http://purl.obolibrary.org/obo/MS_1003947 magnetic sector ion trap instrument ThermoFinnigan MAT900XP Trap MS. http://purl.obolibrary.org/obo/MS_1000175 MAT95XP http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument ThermoFinnigan MAT95XP MS. http://purl.obolibrary.org/obo/MS_1000176 MAT95XP Trap http://purl.obolibrary.org/obo/MS_1003947 magnetic sector ion trap instrument ThermoFinnigan MAT95XP Trap MS. http://purl.obolibrary.org/obo/MS_1000177 microflex http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' microflex: MALDI TOF. http://purl.obolibrary.org/obo/MS_1000178 microTOF LC http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1000179 neptune http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument ThermoFinnigan NEPTUNE MS. http://purl.obolibrary.org/obo/MS_1000180 NG-5400 http://purl.obolibrary.org/obo/MS_1000126 Waters instrument model Waters NG-5400 MS. http://purl.obolibrary.org/obo/MS_1000181 OMEGA http://purl.obolibrary.org/obo/MS_1003948 fourier transform ion cyclotron resonance instrument IonSpec OMEGA MS. http://purl.obolibrary.org/obo/MS_1000182 OMEGA-2001 http://purl.obolibrary.org/obo/MS_1003948 fourier transform ion cyclotron resonance instrument IonSpec OMEGA-2001 MS. http://purl.obolibrary.org/obo/MS_1000183 OmniFlex http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' OmniFlex: MALDI TOF. http://purl.obolibrary.org/obo/MS_1000184 Platform ICP http://purl.obolibrary.org/obo/MS_1000126 Waters instrument model Waters Platform ICP MS. http://purl.obolibrary.org/obo/MS_1000185 PolarisQ http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument ThermoFinnigan PolarisQ MS. http://purl.obolibrary.org/obo/MS_1000186 proteomics solution 1 http://purl.obolibrary.org/obo/MS_1000121 SCIEX instrument model Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS. http://purl.obolibrary.org/obo/MS_1000187 Q TRAP http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument Applied Biosystems/MDS SCIEX Q TRAP MS. http://purl.obolibrary.org/obo/MS_1000188 Q-Tof micro http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based Q-Tof micro. http://purl.obolibrary.org/obo/MS_1000189 Q-Tof Ultima http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based Q-Tof Ultima. http://purl.obolibrary.org/obo/MS_1000190 QSTAR http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Applied Biosystems/MDS SCIEX QSTAR MS. http://purl.obolibrary.org/obo/MS_1000191 quattro micro http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters (triple) quadrupole based micro. http://purl.obolibrary.org/obo/MS_1000192 Quattro Ultima http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters (triple) quadrupole based Ultima. http://purl.obolibrary.org/obo/MS_1000193 Surveyor MSQ http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument ThermoFinnigan Surveyor MSQ MS. http://purl.obolibrary.org/obo/MS_1000194 SymBiot I http://purl.obolibrary.org/obo/MS_1000121 SCIEX instrument model Applied Biosystems/MDS SCIEX SymBiot I MS. http://purl.obolibrary.org/obo/MS_1000195 SymBiot XVI http://purl.obolibrary.org/obo/MS_1000121 SCIEX instrument model Applied Biosystems/MDS SCIEX SymBiot XVI MS. http://purl.obolibrary.org/obo/MS_1000196 TEMPUS TOF http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument ThermoFinnigan TEMPUS TOF MS. http://purl.obolibrary.org/obo/MS_1000197 TRACE DSQ http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument ThermoFinnigan TRACE DSQ MS. http://purl.obolibrary.org/obo/MS_1000198 TRITON http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument ThermoFinnigan TRITON MS. http://purl.obolibrary.org/obo/MS_1000199 TSQ Quantum http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument ThermoFinnigan TSQ Quantum MS. http://purl.obolibrary.org/obo/MS_1000200 ultima http://purl.obolibrary.org/obo/MS_1003948 fourier transform ion cyclotron resonance instrument IonSpec Ultima MS. http://purl.obolibrary.org/obo/MS_1000201 ultraflex http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' ultraflex: MALDI TOF. http://purl.obolibrary.org/obo/MS_1000202 ultraflex TOF/TOF http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF. http://purl.obolibrary.org/obo/MS_1000203 Voyager-DE PRO http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Applied Biosystems/MDS SCIEX Voyager-DE PRO MS. http://purl.obolibrary.org/obo/MS_1000204 Voyager-DE STR http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Applied Biosystems/MDS SCIEX Voyager-DE STR MS. http://purl.obolibrary.org/obo/MS_1000205 selected ion monitoring http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum. http://purl.obolibrary.org/obo/MS_1000206 selected reaction monitoring http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space. http://purl.obolibrary.org/obo/MS_1000210 base peak http://purl.obolibrary.org/obo/MS_1000231 peak The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures. http://purl.obolibrary.org/obo/MS_1000216 field-free region http://purl.obolibrary.org/obo/MS_1000487 ion optics attribute A section of a mass spectrometer in which there are no electric or magnetic fields. http://purl.obolibrary.org/obo/MS_1000221 magnetic deflection http://purl.obolibrary.org/obo/MS_1000597 ion optics type The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer. http://purl.obolibrary.org/obo/MS_1000224 molecular mass http://purl.obolibrary.org/obo/MS_1000861 molecular entity property Mass of a molecule measured in unified atomic mass units (u or Da). http://purl.obolibrary.org/obo/MS_1000227 multiphoton ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type Photoionization of an atom or molecule in which in two or more photons are absorbed. http://purl.obolibrary.org/obo/MS_1000235 total ion current chromatogram http://purl.obolibrary.org/obo/MS_1000810 ion current chromatogram Representation of the total ion current detected in each of a series of mass spectra versus time. http://purl.obolibrary.org/obo/MS_1000236 transmission http://purl.obolibrary.org/obo/MS_1000496 instrument attribute The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region. http://purl.obolibrary.org/obo/MS_1000239 atmospheric pressure matrix-assisted laser desorption ionization http://purl.obolibrary.org/obo/MS_1000240 atmospheric pressure ionization Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer. http://purl.obolibrary.org/obo/MS_1000240 atmospheric pressure ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type Any ionization process in which ions are formed in the gas phase at atmospheric pressure. http://purl.obolibrary.org/obo/MS_1000242 blackbody infrared radiative dissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation. http://purl.obolibrary.org/obo/MS_1000245 charge stripping http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion. http://purl.obolibrary.org/obo/MS_1000246 delayed extraction http://purl.obolibrary.org/obo/MS_1000597 ion optics type The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1000247 desorption ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The formation of ions from a solid or liquid material after the rapid vaporization of that sample. http://purl.obolibrary.org/obo/MS_1000248 direct insertion probe http://purl.obolibrary.org/obo/MS_1000007 inlet type A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization. http://purl.obolibrary.org/obo/MS_1000249 direct liquid introduction http://purl.obolibrary.org/obo/MS_1000007 inlet type A legacy liquid chromatography-mass spectrometry interface in which a minor fraction of the eluate flow is split and introduced through a narrow orifice or diaphragm directly into the ion source, with solvent-mediated chemical ionization. This interface was largely superseded by atmospheric pressure ionization methods. http://purl.obolibrary.org/obo/MS_1000250 electron capture dissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments. http://purl.obolibrary.org/obo/MS_1000253 electron multiplier http://purl.obolibrary.org/obo/MS_1000026 detector type A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons. http://purl.obolibrary.org/obo/MS_1000254 electrostatic energy analyzer http://purl.obolibrary.org/obo/MS_1000443 mass analyzer type A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time. http://purl.obolibrary.org/obo/MS_1000255 flowing afterglow http://purl.obolibrary.org/obo/MS_1000008 ionization type An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa. http://purl.obolibrary.org/obo/MS_1000257 field desorption http://purl.obolibrary.org/obo/MS_1000247 desorption ionization The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization. http://purl.obolibrary.org/obo/MS_1000258 field ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The removal of electrons from any species by interaction with a high electric field. http://purl.obolibrary.org/obo/MS_1000259 glow discharge ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas. http://purl.obolibrary.org/obo/MS_1000262 infrared multiphoton dissociation http://purl.obolibrary.org/obo/MS_1000435 photodissociation Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons. http://purl.obolibrary.org/obo/MS_1000264 ion trap http://purl.obolibrary.org/obo/MS_1000443 mass analyzer type A device for spatially confining ions using electric and magnetic fields alone or in combination. http://purl.obolibrary.org/obo/MS_1000271 Negative Ion chemical ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type Chemical ionization that results in the formation of negative ions. http://purl.obolibrary.org/obo/MS_1000272 neutralization reionization mass spectrometry http://purl.obolibrary.org/obo/MS_1000008 ionization type With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species. http://purl.obolibrary.org/obo/MS_1000273 photoionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended. http://purl.obolibrary.org/obo/MS_1000274 pyrolysis mass spectrometry http://purl.obolibrary.org/obo/MS_1000008 ionization type A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source. http://purl.obolibrary.org/obo/MS_1000275 collision quadrupole http://purl.obolibrary.org/obo/MS_1000597 ion optics type A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation. http://purl.obolibrary.org/obo/MS_1000276 resonance enhanced multiphoton ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species. http://purl.obolibrary.org/obo/MS_1000278 surface enhanced laser desorption ionization http://purl.obolibrary.org/obo/MS_1000406 surface ionization The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization. http://purl.obolibrary.org/obo/MS_1000279 surface enhanced neat desorption http://purl.obolibrary.org/obo/MS_1000406 surface ionization Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface. http://purl.obolibrary.org/obo/MS_1000281 selected ion flow tube http://purl.obolibrary.org/obo/MS_1000597 ion optics type A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions. http://purl.obolibrary.org/obo/MS_1000282 sustained off-resonance irradiation http://purl.obolibrary.org/obo/MS_1000044 dissociation method A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time. http://purl.obolibrary.org/obo/MS_1000284 stored waveform inverse fourier transform http://purl.obolibrary.org/obo/MS_1003213 mass spectrometry acquisition method A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments. http://purl.obolibrary.org/obo/MS_1000285 total ion current http://purl.obolibrary.org/obo/MS_1003058 spectrum property The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum. http://purl.obolibrary.org/obo/MS_1000286 time lag focusing http://purl.obolibrary.org/obo/MS_1000597 ion optics type Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse. http://purl.obolibrary.org/obo/MS_1000288 cyclotron http://purl.obolibrary.org/obo/MS_1000597 ion optics type A device that uses an oscillating electric field and magnetic field to accelerate charged particles. http://purl.obolibrary.org/obo/MS_1000291 linear ion trap http://purl.obolibrary.org/obo/MS_1000264 ion trap A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap. http://purl.obolibrary.org/obo/MS_1000294 mass spectrum http://purl.obolibrary.org/obo/MS_1000559 spectrum type A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z). http://purl.obolibrary.org/obo/MS_1000300 reflectron http://purl.obolibrary.org/obo/MS_1000597 ion optics type A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time. http://purl.obolibrary.org/obo/MS_1000304 accelerating voltage http://purl.obolibrary.org/obo/MS_1000487 ion optics attribute The electrical potential used to impart kinetic energy to ions in a mass spectrometer. http://purl.obolibrary.org/obo/MS_1000307 einzel lens http://purl.obolibrary.org/obo/MS_1000597 ion optics type Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle. http://purl.obolibrary.org/obo/MS_1000308 electric field strength http://purl.obolibrary.org/obo/MS_1000487 ion optics attribute The magnitude of the force per unit charge at a given point in space. http://purl.obolibrary.org/obo/MS_1000309 first stability region http://purl.obolibrary.org/obo/MS_1000597 ion optics type The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole. http://purl.obolibrary.org/obo/MS_1000310 fringing field http://purl.obolibrary.org/obo/MS_1000597 ion optics type The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element. http://purl.obolibrary.org/obo/MS_1000311 kinetic energy analyzer http://purl.obolibrary.org/obo/MS_1000597 ion optics type A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field. http://purl.obolibrary.org/obo/MS_1000319 space charge effect http://purl.obolibrary.org/obo/MS_1000487 ion optics attribute The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time. http://purl.obolibrary.org/obo/MS_1000320 static field http://purl.obolibrary.org/obo/MS_1000597 ion optics type An electric or magnetic field that does not change in time. http://purl.obolibrary.org/obo/MS_1000322 charge inversion mass spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z. http://purl.obolibrary.org/obo/MS_1000325 constant neutral gain spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell. http://purl.obolibrary.org/obo/MS_1000326 constant neutral loss spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. http://purl.obolibrary.org/obo/MS_1000328 e/2 mass spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions. http://purl.obolibrary.org/obo/MS_1000336 neutral loss http://purl.obolibrary.org/obo/MS_1001055 modification parameters The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type). http://purl.obolibrary.org/obo/MS_1000341 precursor ion spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z. http://purl.obolibrary.org/obo/MS_1000343 product ion spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions. http://purl.obolibrary.org/obo/MS_1000345 array detector http://purl.obolibrary.org/obo/MS_1000026 detector type Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector. http://purl.obolibrary.org/obo/MS_1000346 conversion dynode http://purl.obolibrary.org/obo/MS_1000026 detector type A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected. http://purl.obolibrary.org/obo/MS_1000347 dynode http://purl.obolibrary.org/obo/MS_1000026 detector type One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode. http://purl.obolibrary.org/obo/MS_1000348 focal plane collector http://purl.obolibrary.org/obo/MS_1000026 detector type A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. http://purl.obolibrary.org/obo/MS_1000349 ion-to-photon detector http://purl.obolibrary.org/obo/MS_1000026 detector type A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier. http://purl.obolibrary.org/obo/MS_1000350 point collector http://purl.obolibrary.org/obo/MS_1000026 detector type A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially. http://purl.obolibrary.org/obo/MS_1000351 postacceleration detector http://purl.obolibrary.org/obo/MS_1000026 detector type A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector. http://purl.obolibrary.org/obo/MS_1000353 adduct ion http://purl.obolibrary.org/obo/MS_1003055 adduct Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules. http://purl.obolibrary.org/obo/MS_1000380 adiabatic ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state. http://purl.obolibrary.org/obo/MS_1000381 associative ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron. http://purl.obolibrary.org/obo/MS_1000382 atmospheric pressure photoionization http://purl.obolibrary.org/obo/MS_1000240 atmospheric pressure ionization Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. http://purl.obolibrary.org/obo/MS_1000383 autodetachment http://purl.obolibrary.org/obo/MS_1000008 ionization type The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source. http://purl.obolibrary.org/obo/MS_1000384 autoionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source. http://purl.obolibrary.org/obo/MS_1000385 charge exchange ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization. http://purl.obolibrary.org/obo/MS_1000386 chemi-ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization. http://purl.obolibrary.org/obo/MS_1000387 desorption/ionization on silicon http://purl.obolibrary.org/obo/MS_1000247 desorption ionization The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface. http://purl.obolibrary.org/obo/MS_1000388 dissociative ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion. http://purl.obolibrary.org/obo/MS_1000389 electron ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. http://purl.obolibrary.org/obo/MS_1000392 ionization efficiency http://purl.obolibrary.org/obo/MS_1000482 source attribute The ratio of the number of ions formed to the number of electrons, molecules or photons used. http://purl.obolibrary.org/obo/MS_1000393 laser desorption ionization http://purl.obolibrary.org/obo/MS_1000247 desorption ionization The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material. http://purl.obolibrary.org/obo/MS_1000395 liquid secondary ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization. http://purl.obolibrary.org/obo/MS_1000396 membrane inlet http://purl.obolibrary.org/obo/MS_1000007 inlet type A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source. http://purl.obolibrary.org/obo/MS_1000397 microelectrospray http://purl.obolibrary.org/obo/MS_1000073 electrospray ionization Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray. http://purl.obolibrary.org/obo/MS_1000398 nanoelectrospray http://purl.obolibrary.org/obo/MS_1000073 electrospray ionization Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potential on the tip of the electrospray needle and/or a gas pressure to push the sample through the needle. See also electrospray ionization and microelectrospray. http://purl.obolibrary.org/obo/MS_1000399 penning ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited. http://purl.obolibrary.org/obo/MS_1000400 plasma desorption ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. http://purl.obolibrary.org/obo/MS_1000402 secondary ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions. http://purl.obolibrary.org/obo/MS_1000403 soft ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The formation of gas-phase ions without extensive fragmentation. http://purl.obolibrary.org/obo/MS_1000404 spark ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The formation of ions from a solid material by an intermittent electrical discharge. http://purl.obolibrary.org/obo/MS_1000405 surface-assisted laser desorption ionization http://purl.obolibrary.org/obo/MS_1000247 desorption ionization The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization. http://purl.obolibrary.org/obo/MS_1000406 surface ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. http://purl.obolibrary.org/obo/MS_1000407 thermal ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The ionization of a neutral species through contact with a high temperature surface. http://purl.obolibrary.org/obo/MS_1000408 vertical ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state. http://purl.obolibrary.org/obo/MS_1000412 buffer gas http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute An inert gas used for collisional deactivation of internally excited ions. http://purl.obolibrary.org/obo/MS_1000419 collision gas http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute An inert gas used for collisional excitation. The term target gas is not recommended. http://purl.obolibrary.org/obo/MS_1000422 beam-type collision-induced dissociation http://purl.obolibrary.org/obo/MS_1000133 collision-induced dissociation A collision-induced dissociation process that occurs in a beam-type collision cell. http://purl.obolibrary.org/obo/MS_1000433 low-energy collision-induced dissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative. http://purl.obolibrary.org/obo/MS_1000435 photodissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method A process wherein the reactant ion is dissociated as a result of absorption of one or more photons. http://purl.obolibrary.org/obo/MS_1000446 fast ion bombardment http://purl.obolibrary.org/obo/MS_1000008 ionization type The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample. http://purl.obolibrary.org/obo/MS_1000447 LTQ http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Finnigan LTQ MS. http://purl.obolibrary.org/obo/MS_1000448 LTQ FT http://purl.obolibrary.org/obo/MS_1003971 ion trap fourier transform ion cyclotron resonance instrument Finnigan LTQ FT MS. http://purl.obolibrary.org/obo/MS_1000449 LTQ Orbitrap http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Finnigan LTQ Orbitrap MS. http://purl.obolibrary.org/obo/MS_1000450 LXQ http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Finnigan LXQ MS. http://purl.obolibrary.org/obo/MS_1000455 ion selection attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Ion selection properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1000467 1200 series LC/MSD SL http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2. http://purl.obolibrary.org/obo/MS_1000468 6110 Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications. http://purl.obolibrary.org/obo/MS_1000469 6120A Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition. http://purl.obolibrary.org/obo/MS_1000470 6130 Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition. http://purl.obolibrary.org/obo/MS_1000471 6140 Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition. http://purl.obolibrary.org/obo/MS_1000472 6210 Time-of-Flight LC/MS http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. http://purl.obolibrary.org/obo/MS_1000473 6310 Ion Trap LC/MS http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges. http://purl.obolibrary.org/obo/MS_1000474 6320 Ion Trap LC/MS http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. http://purl.obolibrary.org/obo/MS_1000475 6330 Ion Trap LC/MS http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. http://purl.obolibrary.org/obo/MS_1000476 6340 Ion Trap LC/MS http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. http://purl.obolibrary.org/obo/MS_1000477 6410 Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration. http://purl.obolibrary.org/obo/MS_1000478 1200 series LC/MSD VL http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor. http://purl.obolibrary.org/obo/MS_1000483 Thermo Fisher Scientific instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific. http://purl.obolibrary.org/obo/MS_1000484 orbitrap http://purl.obolibrary.org/obo/MS_1000443 mass analyzer type An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer. http://purl.obolibrary.org/obo/MS_1000485 nanospray inlet http://purl.obolibrary.org/obo/MS_1000057 electrospray inlet Nanospray Inlet. http://purl.obolibrary.org/obo/MS_1000486 source potential http://purl.obolibrary.org/obo/MS_1000482 source attribute Potential difference at the MS source in volts. http://purl.obolibrary.org/obo/MS_1000487 ion optics attribute http://purl.obolibrary.org/obo/MS_1000462 ion optics Ion optics involves components that help focus ion streams in mass spectrometry. http://purl.obolibrary.org/obo/MS_1000488 Hitachi instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Hitachi instrument model. http://purl.obolibrary.org/obo/MS_1000489 Varian instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Varian instrument model. http://purl.obolibrary.org/obo/MS_1000490 Agilent instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Agilent instrument model. http://purl.obolibrary.org/obo/MS_1000491 Dionex instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Dionex instrument model. http://purl.obolibrary.org/obo/MS_1000492 Thermo Electron instrument model http://purl.obolibrary.org/obo/MS_1000483 Thermo Fisher Scientific instrument model Thermo Electron Corporation instrument model. http://purl.obolibrary.org/obo/MS_1000493 Finnigan MAT instrument model http://purl.obolibrary.org/obo/MS_1000483 Thermo Fisher Scientific instrument model Finnigan MAT instrument model. http://purl.obolibrary.org/obo/MS_1000494 Thermo Scientific instrument model http://purl.obolibrary.org/obo/MS_1000483 Thermo Fisher Scientific instrument model Thermo Scientific instrument model. http://purl.obolibrary.org/obo/MS_1000495 Applied Biosystems instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Applied Biosystems instrument model. http://purl.obolibrary.org/obo/MS_1000496 instrument attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Instrument properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1000497 zoom scan http://purl.obolibrary.org/obo/MS_1000503 scan attribute Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate. http://purl.obolibrary.org/obo/MS_1000500 scan window upper limit http://purl.obolibrary.org/obo/MS_1000549 selection window attribute The upper m/z bound of a mass spectrometer scan window. http://purl.obolibrary.org/obo/MS_1000501 scan window lower limit http://purl.obolibrary.org/obo/MS_1000549 selection window attribute The lower m/z bound of a mass spectrometer scan window. http://purl.obolibrary.org/obo/MS_1000502 dwell time http://purl.obolibrary.org/obo/MS_1000503 scan attribute The time spent gathering data across a peak. http://purl.obolibrary.org/obo/MS_1000503 scan attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Nonphysical characteristic attributed to a spectrum acquisition scan. http://purl.obolibrary.org/obo/MS_1000504 base peak m/z http://purl.obolibrary.org/obo/MS_1003058 spectrum property M/z value of the signal of highest intensity in the mass spectrum. http://purl.obolibrary.org/obo/MS_1000505 base peak intensity http://purl.obolibrary.org/obo/MS_1003058 spectrum property The intensity of the greatest peak in the mass spectrum. http://purl.obolibrary.org/obo/MS_1000509 activation energy http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute Activation Energy. http://purl.obolibrary.org/obo/MS_1000511 ms level http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute Stage number achieved in a multi stage mass spectrometry acquisition. http://purl.obolibrary.org/obo/MS_1000512 filter string http://purl.obolibrary.org/obo/MS_1000503 scan attribute A string unique to Thermo instrument describing instrument settings for the scan. http://purl.obolibrary.org/obo/MS_1000514 m/z array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of m/z values. http://purl.obolibrary.org/obo/MS_1000515 intensity array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of intensity values. http://purl.obolibrary.org/obo/MS_1000516 charge array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of charge values. http://purl.obolibrary.org/obo/MS_1000517 signal to noise array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of signal-to-noise values. http://purl.obolibrary.org/obo/MS_1000519 32-bit integer http://purl.obolibrary.org/obo/MS_1000518 binary data type Signed 32-bit little-endian integer. http://purl.obolibrary.org/obo/MS_1000520 16-bit float http://purl.obolibrary.org/obo/MS_1000518 binary data type OBSOLETE Signed 16-bit float. http://purl.obolibrary.org/obo/MS_1000521 32-bit float http://purl.obolibrary.org/obo/MS_1000518 binary data type 32-bit precision little-endian floating point conforming to IEEE-754. http://purl.obolibrary.org/obo/MS_1000522 64-bit integer http://purl.obolibrary.org/obo/MS_1000518 binary data type Signed 64-bit little-endian integer. http://purl.obolibrary.org/obo/MS_1000523 64-bit float http://purl.obolibrary.org/obo/MS_1000518 binary data type 64-bit precision little-endian floating point conforming to IEEE-754. http://purl.obolibrary.org/obo/MS_1000526 Waters raw format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Waters data file format found in a Waters RAW directory, generated from an MS acquisition. http://purl.obolibrary.org/obo/MS_1000527 highest observed m/z http://purl.obolibrary.org/obo/MS_1003058 spectrum property Highest m/z value observed in the m/z array. http://purl.obolibrary.org/obo/MS_1000528 lowest observed m/z http://purl.obolibrary.org/obo/MS_1003058 spectrum property Lowest m/z value observed in the m/z array. http://purl.obolibrary.org/obo/MS_1000529 instrument serial number http://purl.obolibrary.org/obo/MS_1000496 instrument attribute Serial Number of the instrument. http://purl.obolibrary.org/obo/MS_1000530 file format conversion http://purl.obolibrary.org/obo/MS_1000452 data transformation Conversion of one file format to another. http://purl.obolibrary.org/obo/MS_1000532 Xcalibur http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Finnigan software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000533 Bioworks http://purl.obolibrary.org/obo/MS_1001457 data processing software Thermo Finnigan software for data analysis of peptides and proteins. http://purl.obolibrary.org/obo/MS_1000534 MassLynx http://purl.obolibrary.org/obo/MS_1001457 data processing software Micromass software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000535 FlexAnalysis http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker software for data analysis. http://purl.obolibrary.org/obo/MS_1000536 Data Explorer http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000537 4700 Explorer http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000538 massWolf http://purl.obolibrary.org/obo/MS_1001457 data processing software A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology. http://purl.obolibrary.org/obo/MS_1000539 Voyager Biospectrometry Workstation System http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems MALDI-TOF data acquisition and analysis system. http://purl.obolibrary.org/obo/MS_1000540 FlexControl http://purl.obolibrary.org/obo/MS_1001455 acquisition software Bruker software for data acquisition. http://purl.obolibrary.org/obo/MS_1000541 ReAdW http://purl.obolibrary.org/obo/MS_1001457 data processing software A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced "readraw". http://purl.obolibrary.org/obo/MS_1000542 MzStar http://purl.obolibrary.org/obo/MS_1001457 data processing software A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program. http://purl.obolibrary.org/obo/MS_1000543 data processing action http://purl.obolibrary.org/obo/MS_1000452 data transformation Data processing attribute used to describe the type of data processing performed on the data file. http://purl.obolibrary.org/obo/MS_1000544 Conversion to mzML http://purl.obolibrary.org/obo/MS_1000530 file format conversion Conversion of a file format to Proteomics Standards Initiative mzML file format. http://purl.obolibrary.org/obo/MS_1000545 Conversion to mzXML http://purl.obolibrary.org/obo/MS_1000530 file format conversion Conversion of a file format to Institute of Systems Biology mzXML file format. http://purl.obolibrary.org/obo/MS_1000546 Conversion to mzData http://purl.obolibrary.org/obo/MS_1000530 file format conversion Conversion of a file format to Proteomics Standards Initiative mzData file format. http://purl.obolibrary.org/obo/MS_1000548 sample attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Sample properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1000549 selection window attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Selection window properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1000551 Analyst http://purl.obolibrary.org/obo/MS_1001457 data processing software SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition. http://purl.obolibrary.org/obo/MS_1000553 Trapper http://purl.obolibrary.org/obo/MS_1001457 data processing software A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology. http://purl.obolibrary.org/obo/MS_1000554 LCQ Deca http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument ThermoFinnigan LCQ Deca. http://purl.obolibrary.org/obo/MS_1000555 LTQ Orbitrap Discovery http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument LTQ Orbitrap Discovery. http://purl.obolibrary.org/obo/MS_1000556 LTQ Orbitrap XL http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument LTQ Orbitrap XL. http://purl.obolibrary.org/obo/MS_1000557 LTQ FT Ultra http://purl.obolibrary.org/obo/MS_1003971 ion trap fourier transform ion cyclotron resonance instrument LTQ FT Ultra. http://purl.obolibrary.org/obo/MS_1000558 GC Quantum http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument GC Quantum. http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format http://purl.obolibrary.org/obo/MS_1001459 file format The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. http://purl.obolibrary.org/obo/MS_1000562 ABI WIFF format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Applied Biosystems WIFF file format. http://purl.obolibrary.org/obo/MS_1000563 Thermo RAW format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Thermo Scientific RAW file format. http://purl.obolibrary.org/obo/MS_1000564 PSI mzData format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Proteomics Standards Initiative mzData file format. http://purl.obolibrary.org/obo/MS_1000565 Micromass PKL format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Micromass PKL file format. http://purl.obolibrary.org/obo/MS_1000566 ISB mzXML format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Institute of Systems Biology mzXML file format. http://purl.obolibrary.org/obo/MS_1000567 Bruker/Agilent YEP format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Bruker/Agilent YEP file format. http://purl.obolibrary.org/obo/MS_1000568 MD5 http://purl.obolibrary.org/obo/MS_1000561 data file checksum type MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files. http://purl.obolibrary.org/obo/MS_1000569 SHA-1 http://purl.obolibrary.org/obo/MS_1000561 data file checksum type SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard. http://purl.obolibrary.org/obo/MS_1000571 sum of spectra http://purl.obolibrary.org/obo/MS_1000570 spectra combination Spectra Sum. http://purl.obolibrary.org/obo/MS_1000573 median of spectra http://purl.obolibrary.org/obo/MS_1000570 spectra combination Spectra is combined by calculating the median of the spectra. http://purl.obolibrary.org/obo/MS_1000574 zlib compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Zlib. http://purl.obolibrary.org/obo/MS_1000575 mean of spectra http://purl.obolibrary.org/obo/MS_1000570 spectra combination Spectra is combined by calculating the mean of the spectra. http://purl.obolibrary.org/obo/MS_1000576 no compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type No Compression. http://purl.obolibrary.org/obo/MS_1000577 source data file http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute Data file from which an entity is sourced. http://purl.obolibrary.org/obo/MS_1000578 LCQ Fleet http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument LCQ Fleet. http://purl.obolibrary.org/obo/MS_1000579 MS1 spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment. http://purl.obolibrary.org/obo/MS_1000580 MSn spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n. http://purl.obolibrary.org/obo/MS_1000581 CRM spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. http://purl.obolibrary.org/obo/MS_1000582 SIM spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring). http://purl.obolibrary.org/obo/MS_1000583 SRM spectrum http://purl.obolibrary.org/obo/MS_1000294 mass spectrum Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space. http://purl.obolibrary.org/obo/MS_1000584 mzML format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Proteomics Standards Initiative mzML file format. http://purl.obolibrary.org/obo/MS_1000585 contact attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Details about a person or organization to contact in case of concern or discussion about the file. http://purl.obolibrary.org/obo/MS_1000586 contact name http://purl.obolibrary.org/obo/MS_1000585 contact attribute Name of the contact person or organization. http://purl.obolibrary.org/obo/MS_1000587 contact address http://purl.obolibrary.org/obo/MS_1000585 contact attribute Postal address of the contact person or organization. http://purl.obolibrary.org/obo/MS_1000588 contact URL http://purl.obolibrary.org/obo/MS_1000585 contact attribute Uniform Resource Locator related to the contact person or organization. http://purl.obolibrary.org/obo/MS_1000589 contact email http://purl.obolibrary.org/obo/MS_1000585 contact attribute Email address of the contact person or organization. http://purl.obolibrary.org/obo/MS_1000590 contact affiliation http://purl.obolibrary.org/obo/MS_1000585 contact attribute Home institution of the contact person. http://purl.obolibrary.org/obo/MS_1000591 MzWiff http://purl.obolibrary.org/obo/MS_1001457 data processing software A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program. http://purl.obolibrary.org/obo/MS_1000592 smoothing http://purl.obolibrary.org/obo/MS_1000543 data processing action A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process. http://purl.obolibrary.org/obo/MS_1000593 baseline reduction http://purl.obolibrary.org/obo/MS_1000543 data processing action A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparison between intensities of m/z values. http://purl.obolibrary.org/obo/MS_1000594 low intensity data point removal http://purl.obolibrary.org/obo/MS_1001486 data filtering The removal of very low intensity data points that are likely to be spurious noise rather than real signal. http://purl.obolibrary.org/obo/MS_1000595 time array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of relative time offset values from a reference time. http://purl.obolibrary.org/obo/MS_1000597 ion optics type http://purl.obolibrary.org/obo/MS_1000462 ion optics The electrical potential used to impart kinetic energy to ions in a mass spectrometer. http://purl.obolibrary.org/obo/MS_1000598 electron transfer dissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions. http://purl.obolibrary.org/obo/MS_1000599 pulsed q dissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected. http://purl.obolibrary.org/obo/MS_1000600 Proteios http://purl.obolibrary.org/obo/MS_1001457 data processing software Database application and analysis platform for proteomics. http://purl.obolibrary.org/obo/MS_1000601 ProteinLynx Global Server http://purl.obolibrary.org/obo/MS_1001457 data processing software Waters software for data analysis. http://purl.obolibrary.org/obo/MS_1000602 Shimadzu MALDI-TOF instrument model http://purl.obolibrary.org/obo/MS_1000124 Shimadzu instrument model Shimadzu MALDI-TOF instrument model. http://purl.obolibrary.org/obo/MS_1000603 Shimadzu Scientific Instruments instrument model http://purl.obolibrary.org/obo/MS_1000124 Shimadzu instrument model Shimadzu Scientific Instruments instrument model. http://purl.obolibrary.org/obo/MS_1000604 LCMS-IT-TOF http://purl.obolibrary.org/obo/MS_1003764 ion trap time-of-flight instrument Shimadzu Scientific Instruments LCMS-IT-TOF MS. http://purl.obolibrary.org/obo/MS_1000605 LCMS-2010EV http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu Scientific Instruments LCMS-2010EV MS. http://purl.obolibrary.org/obo/MS_1000606 LCMS-2010A http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu Scientific Instruments LCMS-2010A MS. http://purl.obolibrary.org/obo/MS_1000607 AXIMA CFR MALDI-TOF http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Shimadzu Biotech AXIMA CFR MALDI-TOF MS. http://purl.obolibrary.org/obo/MS_1000608 AXIMA-QIT http://purl.obolibrary.org/obo/MS_1003764 ion trap time-of-flight instrument Shimadzu Biotech AXIMA-QIT MS. http://purl.obolibrary.org/obo/MS_1000609 AXIMA-CFR plus http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Shimadzu Biotech AXIMA-CFR plus MS. http://purl.obolibrary.org/obo/MS_1000610 AXIMA Performance MALDI-TOF/TOF http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS. http://purl.obolibrary.org/obo/MS_1000611 AXIMA Confidence MALDI-TOF http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS. http://purl.obolibrary.org/obo/MS_1000612 AXIMA Assurance Linear MALDI-TOF http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS. http://purl.obolibrary.org/obo/MS_1000613 DTA format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format SEQUEST DTA file format. http://purl.obolibrary.org/obo/MS_1000614 ProteinLynx Global Server mass spectrum XML format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Peak list file format used by ProteinLynx Global Server. http://purl.obolibrary.org/obo/MS_1000615 ProteoWizard software http://purl.obolibrary.org/obo/MS_1001457 data processing software ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb. http://purl.obolibrary.org/obo/MS_1000616 preset scan configuration http://purl.obolibrary.org/obo/MS_1000503 scan attribute A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo "scan event", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time. http://purl.obolibrary.org/obo/MS_1000617 wavelength array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of electromagnetic radiation wavelength values. http://purl.obolibrary.org/obo/MS_1000618 highest observed wavelength http://purl.obolibrary.org/obo/MS_1003058 spectrum property Highest wavelength observed in an EMR spectrum. http://purl.obolibrary.org/obo/MS_1000619 lowest observed wavelength http://purl.obolibrary.org/obo/MS_1003058 spectrum property Lowest wavelength observed in an EMR spectrum. http://purl.obolibrary.org/obo/MS_1000620 PDA spectrum http://purl.obolibrary.org/obo/MS_1000559 spectrum type OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum). http://purl.obolibrary.org/obo/MS_1000621 photodiode array detector http://purl.obolibrary.org/obo/MS_1000345 array detector An array detector used to record spectra in the ultraviolet and visible region of light. http://purl.obolibrary.org/obo/MS_1000622 Surveyor PDA http://purl.obolibrary.org/obo/MS_1000494 Thermo Scientific instrument model Surveyor PDA. http://purl.obolibrary.org/obo/MS_1000623 Accela PDA http://purl.obolibrary.org/obo/MS_1000494 Thermo Scientific instrument model Accela PDA. http://purl.obolibrary.org/obo/MS_1000624 inductive detector http://purl.obolibrary.org/obo/MS_1000026 detector type Inductive detector. http://purl.obolibrary.org/obo/MS_1000627 selected ion current chromatogram http://purl.obolibrary.org/obo/MS_1000810 ion current chromatogram Representation of an array of the measurements of a specific single ion current versus time. http://purl.obolibrary.org/obo/MS_1000628 basepeak chromatogram http://purl.obolibrary.org/obo/MS_1000810 ion current chromatogram Representation of an array of the most intense peaks versus time. http://purl.obolibrary.org/obo/MS_1000629 low intensity threshold http://purl.obolibrary.org/obo/MS_1000630 data processing parameter Threshold below which some action is taken. http://purl.obolibrary.org/obo/MS_1000631 high intensity threshold http://purl.obolibrary.org/obo/MS_1000630 data processing parameter Threshold above which some action is taken. http://purl.obolibrary.org/obo/MS_1000632 Q-Tof Premier http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based Q-Tof Premier. http://purl.obolibrary.org/obo/MS_1000633 possible charge state http://purl.obolibrary.org/obo/MS_1000455 ion selection attribute A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty. http://purl.obolibrary.org/obo/MS_1000634 DSQ http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument ThermoFinnigan DSQ GC-MS. http://purl.obolibrary.org/obo/MS_1000635 ITQ 700 http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Scientific ITQ 700 GC-MS. http://purl.obolibrary.org/obo/MS_1000636 ITQ 900 http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Scientific ITQ 900 GC-MS. http://purl.obolibrary.org/obo/MS_1000637 ITQ 1100 http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Scientific ITQ 1100 GC-MS. http://purl.obolibrary.org/obo/MS_1000638 LTQ XL ETD http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Scientific LTQ XL MS with ETD. http://purl.obolibrary.org/obo/MS_1000639 LTQ Orbitrap XL ETD http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Thermo Scientific LTQ Orbitrap XL MS with ETD. http://purl.obolibrary.org/obo/MS_1000640 DFS http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Thermo Scientific DFS HR GC-MS. http://purl.obolibrary.org/obo/MS_1000641 DSQ II http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Thermo Scientific DSQ II GC-MS. http://purl.obolibrary.org/obo/MS_1000642 MALDI LTQ XL http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Scientific MALDI LTQ XL MS. http://purl.obolibrary.org/obo/MS_1000643 MALDI LTQ Orbitrap http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Thermo Scientific MALDI LTQ Orbitrap MS. http://purl.obolibrary.org/obo/MS_1000644 TSQ Quantum Access http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ Quantum Access MS. http://purl.obolibrary.org/obo/MS_1000645 Element XR http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Thermo Scientific Element XR HR-ICP-MS. http://purl.obolibrary.org/obo/MS_1000646 Element 2 http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Thermo Scientific Element 2 HR-ICP-MS. http://purl.obolibrary.org/obo/MS_1000647 Element GD http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Thermo Scientific Element GD Glow Discharge MS. http://purl.obolibrary.org/obo/MS_1000648 GC IsoLink http://purl.obolibrary.org/obo/MS_1000494 Thermo Scientific instrument model Thermo Scientific GC IsoLink Isotope Ratio MS. http://purl.obolibrary.org/obo/MS_1000649 Exactive http://purl.obolibrary.org/obo/MS_1003953 orbitrap instrument Thermo Scientific Exactive MS. http://purl.obolibrary.org/obo/MS_1000650 Proteome Discoverer http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific software for data analysis of peptides and proteins. http://purl.obolibrary.org/obo/MS_1000651 3200 QTRAP http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200. http://purl.obolibrary.org/obo/MS_1000652 4800 Plus MALDI TOF/TOF http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer. http://purl.obolibrary.org/obo/MS_1000653 API 3200 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS. http://purl.obolibrary.org/obo/MS_1000654 API 5000 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS. http://purl.obolibrary.org/obo/MS_1000655 QSTAR Elite http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite. http://purl.obolibrary.org/obo/MS_1000656 QSTAR Pulsar http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Applied Biosystems|MDS SCIEX QSTAR Pulsar. http://purl.obolibrary.org/obo/MS_1000657 QSTAR XL http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Applied Biosystems|MDS SCIEX QSTAR XL. http://purl.obolibrary.org/obo/MS_1000658 4800 Proteomics Analyzer http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer. http://purl.obolibrary.org/obo/MS_1000659 4000 Series Explorer Software http://purl.obolibrary.org/obo/MS_1001457 data processing software SCIEX or Applied Biosystems software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000661 GPS Explorer http://purl.obolibrary.org/obo/MS_1001457 data processing software SCIEX or Applied Biosystems software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000662 LightSight Software http://purl.obolibrary.org/obo/MS_1001457 data processing software SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification. http://purl.obolibrary.org/obo/MS_1000663 ProteinPilot Software http://purl.obolibrary.org/obo/MS_1001457 data processing software SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant. http://purl.obolibrary.org/obo/MS_1000664 TissueView Software http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems|MDS SCIEX software for tissue imaging. http://purl.obolibrary.org/obo/MS_1000665 MarkerView Software http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling. http://purl.obolibrary.org/obo/MS_1000666 MRMPilot Software http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems|MDS SCIEX software for MRM assay development. http://purl.obolibrary.org/obo/MS_1000667 BioAnalyst http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems|MDS SCIEX software for bio-related data exploration. http://purl.obolibrary.org/obo/MS_1000668 Pro ID http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems|MDS SCIEX software for protein identification. http://purl.obolibrary.org/obo/MS_1000669 Pro ICAT http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT. http://purl.obolibrary.org/obo/MS_1000670 Pro Quant http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ. http://purl.obolibrary.org/obo/MS_1000671 Pro BLAST http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems|MDS SCIEX software for MS-BLAST identification. http://purl.obolibrary.org/obo/MS_1000672 Cliquid http://purl.obolibrary.org/obo/MS_1000690 SCIEX software SCIEX Cliquid software for data analysis and quantitation. http://purl.obolibrary.org/obo/MS_1000673 MIDAS Workflow Designer http://purl.obolibrary.org/obo/MS_1000690 SCIEX software Applied Biosystems|MDS SCIEX software for MRM assay development. http://purl.obolibrary.org/obo/MS_1000674 MultiQuant http://purl.obolibrary.org/obo/MS_1001457 data processing software Applied Biosystems|MDS SCIEX software for MRM-based quantitation. http://purl.obolibrary.org/obo/MS_1000675 6220 Time-of-Flight LC/MS http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. http://purl.obolibrary.org/obo/MS_1000676 6510 Quadrupole Time-of-Flight LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. http://purl.obolibrary.org/obo/MS_1000677 6520A Quadrupole Time-of-Flight LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. http://purl.obolibrary.org/obo/MS_1000678 MassHunter Data Acquisition http://purl.obolibrary.org/obo/MS_1001455 acquisition software Software for data acquisition of 6000 series instruments. http://purl.obolibrary.org/obo/MS_1000679 MassHunter Easy Access http://purl.obolibrary.org/obo/MS_1001455 acquisition software Software for open access data acquisition. http://purl.obolibrary.org/obo/MS_1000680 MassHunter Qualitative Analysis http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for data analysis of data from 6000 series instruments. http://purl.obolibrary.org/obo/MS_1000681 MassHunter Quantitative Analysis http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data. http://purl.obolibrary.org/obo/MS_1000682 MassHunter Metabolite ID http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for identification of metabolites. http://purl.obolibrary.org/obo/MS_1000683 MassHunter BioConfirm http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for protein characterization. http://purl.obolibrary.org/obo/MS_1000684 Genespring MS http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. http://purl.obolibrary.org/obo/MS_1000685 MassHunter Mass Profiler http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. http://purl.obolibrary.org/obo/MS_1000686 METLIN http://purl.obolibrary.org/obo/MS_1001457 data processing software Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites. http://purl.obolibrary.org/obo/MS_1000687 Spectrum Mill for MassHunter Workstation http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for protein identification and characterization of complex protein digest mixtures. http://purl.obolibrary.org/obo/MS_1000688 6300 Series Ion Trap Data Analysis Software http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for data analysis of 6300 series ion trap mass spectrometers. http://purl.obolibrary.org/obo/MS_1000689 Agilent software http://purl.obolibrary.org/obo/MS_1000531 software Agilent software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000690 SCIEX software http://purl.obolibrary.org/obo/MS_1000531 software SCIEX or Applied Biosystems software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000691 Applied Biosystems software http://purl.obolibrary.org/obo/MS_1000531 software Applied Biosystems|MDS SCIEX software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000692 Bruker software http://purl.obolibrary.org/obo/MS_1000531 software Bruker software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000693 Thermo Finnigan software http://purl.obolibrary.org/obo/MS_1000531 software Thermo Finnigan software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000694 Waters software http://purl.obolibrary.org/obo/MS_1000531 software Waters software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1000695 apex ultra http://purl.obolibrary.org/obo/MS_1003766 quadrupole fourier transform ion cyclotron resonance instrument Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. http://purl.obolibrary.org/obo/MS_1000696 autoflex III smartbeam http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' autoflex III smartbeam: MALDI TOF. http://purl.obolibrary.org/obo/MS_1000697 Bruker Daltonics HCT Series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' HCT Series. http://purl.obolibrary.org/obo/MS_1000698 HCTultra http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1000699 HCTultra PTM http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR. http://purl.obolibrary.org/obo/MS_1000700 HCTultra ETD II http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD. http://purl.obolibrary.org/obo/MS_1000701 microflex LT http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' microflex LT: MALDI TOF. http://purl.obolibrary.org/obo/MS_1000702 micrOTOF http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI. http://purl.obolibrary.org/obo/MS_1000703 micrOTOF-Q http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1000704 micrOTOF-Q II http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1000705 ultraflex III TOF/TOF http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF. http://purl.obolibrary.org/obo/MS_1000706 apexControl http://purl.obolibrary.org/obo/MS_1001455 acquisition software Bruker software for data acquisition. http://purl.obolibrary.org/obo/MS_1000707 BioTools http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker software for data analysis. http://purl.obolibrary.org/obo/MS_1000708 CLINPROT http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker CLINPROT software. http://purl.obolibrary.org/obo/MS_1000709 CLINPROT micro http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker CLINPROT micro software. http://purl.obolibrary.org/obo/MS_1000710 CLINPROT robot http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker CLINPROT robot software. http://purl.obolibrary.org/obo/MS_1000711 ClinProTools http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker ClinProTools software. http://purl.obolibrary.org/obo/MS_1000712 Compass http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker Compass software. http://purl.obolibrary.org/obo/MS_1000713 Compass for HCT/esquire http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker Compass for HCT/esquire software. http://purl.obolibrary.org/obo/MS_1000714 Compass for micrOTOF http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker Compass for micrOTOF software. http://purl.obolibrary.org/obo/MS_1000715 Compass OpenAccess http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker compass OpenAccess software. http://purl.obolibrary.org/obo/MS_1000716 Compass Security Pack http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker compass Security Pack software. http://purl.obolibrary.org/obo/MS_1000717 CompassXport http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker stand-alone software for data conversion. http://purl.obolibrary.org/obo/MS_1000718 CompassXtract http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker software library for data access. http://purl.obolibrary.org/obo/MS_1000719 DataAnalysis http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker software for data analysis. http://purl.obolibrary.org/obo/MS_1000720 dpControl http://purl.obolibrary.org/obo/MS_1001455 acquisition software Bruker software for data acquisition. http://purl.obolibrary.org/obo/MS_1000721 esquireControl http://purl.obolibrary.org/obo/MS_1001455 acquisition software Bruker software for data acquisition. http://purl.obolibrary.org/obo/MS_1000722 flexImaging http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker software for data analysis. http://purl.obolibrary.org/obo/MS_1000723 GENOLINK http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker GENOLINK software. http://purl.obolibrary.org/obo/MS_1000724 GenoTools http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker GenoTools software. http://purl.obolibrary.org/obo/MS_1000725 HCTcontrol http://purl.obolibrary.org/obo/MS_1001455 acquisition software Bruker software for data acquisition. http://purl.obolibrary.org/obo/MS_1000726 micrOTOFcontrol http://purl.obolibrary.org/obo/MS_1001455 acquisition software Bruker software for data acquisition. http://purl.obolibrary.org/obo/MS_1000727 PolyTools http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker PolyTools software. http://purl.obolibrary.org/obo/MS_1000728 ProfileAnalysis http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker software for data analysis. http://purl.obolibrary.org/obo/MS_1000729 PROTEINEER http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker PROTEINEER software. http://purl.obolibrary.org/obo/MS_1000730 PROTEINEER dp http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker PROTEINEER dp software. http://purl.obolibrary.org/obo/MS_1000731 PROTEINEER fc http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker PROTEINEER fc software. http://purl.obolibrary.org/obo/MS_1000732 PROTEINEER spII http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker PROTEINEER spII software. http://purl.obolibrary.org/obo/MS_1000733 PROTEINEER-LC http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker PROTEINEER-LC software. http://purl.obolibrary.org/obo/MS_1000734 ProteinScape http://purl.obolibrary.org/obo/MS_1001456 analysis software Bruker ProteinScape software. http://purl.obolibrary.org/obo/MS_1000735 PureDisk http://purl.obolibrary.org/obo/MS_1000692 Bruker software BrukerPureDisk software. http://purl.obolibrary.org/obo/MS_1000736 QuantAnalysis http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker software for data analysis. http://purl.obolibrary.org/obo/MS_1000737 spControl http://purl.obolibrary.org/obo/MS_1001455 acquisition software Bruker software for data acquisition. http://purl.obolibrary.org/obo/MS_1000738 TargetAnalysis http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker TargetAnalysis software. http://purl.obolibrary.org/obo/MS_1000739 WARP-LC http://purl.obolibrary.org/obo/MS_1001139 quantitation software name Bruker WARP-LC software. http://purl.obolibrary.org/obo/MS_1000740 parameter file http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Parameter file used to configure the acquisition of raw data on the instrument. http://purl.obolibrary.org/obo/MS_1000741 Conversion to dta http://purl.obolibrary.org/obo/MS_1000530 file format conversion Conversion to dta format. http://purl.obolibrary.org/obo/MS_1000742 Bioworks SRF format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Thermo Finnigan SRF file format. http://purl.obolibrary.org/obo/MS_1000743 TSQ Quantum Ultra AM http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ Quantum Ultra AM. http://purl.obolibrary.org/obo/MS_1000744 selected ion m/z http://purl.obolibrary.org/obo/MS_1000455 ion selection attribute Mass-to-charge ratio of an selected ion. http://purl.obolibrary.org/obo/MS_1000745 retention time alignment http://purl.obolibrary.org/obo/MS_1000543 data processing action The correction of the spectrum scan times, as used e.g. in label-free proteomics. http://purl.obolibrary.org/obo/MS_1000746 high intensity data point removal http://purl.obolibrary.org/obo/MS_1001486 data filtering The removal of very high intensity data points. http://purl.obolibrary.org/obo/MS_1000747 completion time http://purl.obolibrary.org/obo/MS_1000630 data processing parameter The time that a data processing action was finished. http://purl.obolibrary.org/obo/MS_1000748 SSQ 7000 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument ThermoFinnigan SSQ 7000 MS. http://purl.obolibrary.org/obo/MS_1000749 TSQ 7000 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument ThermoFinnigan TSQ 7000 MS. http://purl.obolibrary.org/obo/MS_1000750 TSQ http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument ThermoFinnigan TSQ MS. http://purl.obolibrary.org/obo/MS_1000751 TSQ Quantum Ultra http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ Quantum Ultra. http://purl.obolibrary.org/obo/MS_1000752 TOPP software http://purl.obolibrary.org/obo/MS_1001457 data processing software TOPP (The OpenMS proteomics pipeline) software. http://purl.obolibrary.org/obo/MS_1000753 BaselineFilter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Removes the baseline from profile spectra using a top-hat filter. http://purl.obolibrary.org/obo/MS_1000754 DBExporter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Exports data from an OpenMS database to a file. http://purl.obolibrary.org/obo/MS_1000755 DBImporter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Imports data to an OpenMS database. http://purl.obolibrary.org/obo/MS_1000756 FileConverter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Converts between different MS file formats. http://purl.obolibrary.org/obo/MS_1000757 FileFilter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Extracts or manipulates portions of data from peak, feature or consensus feature files. http://purl.obolibrary.org/obo/MS_1000758 FileMerger http://purl.obolibrary.org/obo/MS_1000752 TOPP software Merges several MS files into one file. http://purl.obolibrary.org/obo/MS_1000759 InternalCalibration http://purl.obolibrary.org/obo/MS_1000752 TOPP software Applies an internal calibration. http://purl.obolibrary.org/obo/MS_1000760 MapAligner http://purl.obolibrary.org/obo/MS_1000752 TOPP software OBSOLETE Corrects retention time distortions between maps. http://purl.obolibrary.org/obo/MS_1000761 MapNormalizer http://purl.obolibrary.org/obo/MS_1000752 TOPP software Normalizes peak intensities in an MS run. http://purl.obolibrary.org/obo/MS_1000762 NoiseFilter http://purl.obolibrary.org/obo/MS_1000752 TOPP software OBSOLETE Removes noise from profile spectra by using different smoothing techniques. http://purl.obolibrary.org/obo/MS_1000763 PeakPicker http://purl.obolibrary.org/obo/MS_1000752 TOPP software OBSOLETE Finds mass spectrometric peaks in profile mass spectra. http://purl.obolibrary.org/obo/MS_1000764 Resampler http://purl.obolibrary.org/obo/MS_1000752 TOPP software Transforms an LC/MS map into a resampled map or a png image. http://purl.obolibrary.org/obo/MS_1000765 SpectraFilter http://purl.obolibrary.org/obo/MS_1000752 TOPP software OBSOLETE Applies a filter to peak spectra. http://purl.obolibrary.org/obo/MS_1000766 TOFCalibration http://purl.obolibrary.org/obo/MS_1000752 TOPP software Applies time of flight calibration. http://purl.obolibrary.org/obo/MS_1000768 Thermo nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger. http://purl.obolibrary.org/obo/MS_1000769 Waters nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1000770 WIFF nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1000771 Bruker/Agilent YEP nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by scan=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1000772 Bruker BAF nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by scan=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1000773 Bruker FID nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by file=xsd:IDREF. http://purl.obolibrary.org/obo/MS_1000774 multiple peak list nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by index=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1000775 single peak list nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by file=xsd:IDREF. http://purl.obolibrary.org/obo/MS_1000776 scan number only nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by scan=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1000777 spectrum identifier nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by spectrum=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1000778 charge state calculation http://purl.obolibrary.org/obo/MS_1000543 data processing action A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm. http://purl.obolibrary.org/obo/MS_1000779 below precursor intensity dominance charge state calculation http://purl.obolibrary.org/obo/MS_1000778 charge state calculation Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z. http://purl.obolibrary.org/obo/MS_1000780 precursor recalculation http://purl.obolibrary.org/obo/MS_1000543 data processing action A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions. http://purl.obolibrary.org/obo/MS_1000781 msPrefix precursor recalculation http://purl.obolibrary.org/obo/MS_1000780 precursor recalculation Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans. http://purl.obolibrary.org/obo/MS_1000782 Savitzky-Golay smoothing http://purl.obolibrary.org/obo/MS_1000592 smoothing Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques. http://purl.obolibrary.org/obo/MS_1000783 LOWESS smoothing http://purl.obolibrary.org/obo/MS_1000592 smoothing Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible. http://purl.obolibrary.org/obo/MS_1000784 Gaussian smoothing http://purl.obolibrary.org/obo/MS_1000592 smoothing Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function. http://purl.obolibrary.org/obo/MS_1000785 moving average smoothing http://purl.obolibrary.org/obo/MS_1000592 smoothing Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect. http://purl.obolibrary.org/obo/MS_1000786 non-standard data array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added. http://purl.obolibrary.org/obo/MS_1000787 inclusive low intensity threshold http://purl.obolibrary.org/obo/MS_1000630 data processing parameter Threshold at or below which some action is taken. http://purl.obolibrary.org/obo/MS_1000788 inclusive high intensity threshold http://purl.obolibrary.org/obo/MS_1000630 data processing parameter Threshold at or above which some action is taken. http://purl.obolibrary.org/obo/MS_1000789 enhanced multiply charged spectrum http://purl.obolibrary.org/obo/MS_1000579 MS1 spectrum MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions. http://purl.obolibrary.org/obo/MS_1000790 time-delayed fragmentation spectrum http://purl.obolibrary.org/obo/MS_1000580 MSn spectrum MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation. http://purl.obolibrary.org/obo/MS_1000792 isolation window attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Isolation window parameter. http://purl.obolibrary.org/obo/MS_1000793 isolation window upper limit http://purl.obolibrary.org/obo/MS_1000792 isolation window attribute OBSOLETE The highest m/z being isolated in an isolation window. http://purl.obolibrary.org/obo/MS_1000794 isolation window lower limit http://purl.obolibrary.org/obo/MS_1000792 isolation window attribute OBSOLETE The lowest m/z being isolated in an isolation window. http://purl.obolibrary.org/obo/MS_1000795 no combination http://purl.obolibrary.org/obo/MS_1000570 spectra combination Use this term if only one scan was recorded or there is no information about scans available. http://purl.obolibrary.org/obo/MS_1000796 spectrum title http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file. http://purl.obolibrary.org/obo/MS_1000797 peak list scans http://purl.obolibrary.org/obo/MS_1003058 spectrum property A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. http://purl.obolibrary.org/obo/MS_1000798 peak list raw scans http://purl.obolibrary.org/obo/MS_1003058 spectrum property A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. http://purl.obolibrary.org/obo/MS_1000799 custom unreleased software tool http://purl.obolibrary.org/obo/MS_1000531 software A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added. http://purl.obolibrary.org/obo/MS_1000800 mass resolving power http://purl.obolibrary.org/obo/MS_1000503 scan attribute The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported. http://purl.obolibrary.org/obo/MS_1000801 area peak picking http://purl.obolibrary.org/obo/MS_1000035 peak picking Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported. http://purl.obolibrary.org/obo/MS_1000802 height peak picking http://purl.obolibrary.org/obo/MS_1000035 peak picking Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported. http://purl.obolibrary.org/obo/MS_1000803 analyzer scan offset http://purl.obolibrary.org/obo/MS_1000503 scan attribute Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value. http://purl.obolibrary.org/obo/MS_1000804 electromagnetic radiation spectrum http://purl.obolibrary.org/obo/MS_1000559 spectrum type A plot of the relative intensity of electromagnetic radiation as a function of the wavelength. http://purl.obolibrary.org/obo/MS_1000805 emission spectrum http://purl.obolibrary.org/obo/MS_1000559 spectrum type A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited. http://purl.obolibrary.org/obo/MS_1000806 absorption spectrum http://purl.obolibrary.org/obo/MS_1000559 spectrum type A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited. http://purl.obolibrary.org/obo/MS_1000807 Th/s http://purl.obolibrary.org/obo/UO_0000000 unit Unit describing the scan rate of a spectrum in Thomson per second. http://purl.obolibrary.org/obo/MS_1000808 chromatogram attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Chromatogram properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1000809 chromatogram title http://purl.obolibrary.org/obo/MS_1000808 chromatogram attribute A free-form text title describing a chromatogram. http://purl.obolibrary.org/obo/MS_1000810 ion current chromatogram http://purl.obolibrary.org/obo/MS_1000626 chromatogram type Representation of the current of ions versus time. http://purl.obolibrary.org/obo/MS_1000811 electromagnetic radiation chromatogram http://purl.obolibrary.org/obo/MS_1000626 chromatogram type Representation of electromagnetic properties versus time. http://purl.obolibrary.org/obo/MS_1000812 absorption chromatogram http://purl.obolibrary.org/obo/MS_1000811 electromagnetic radiation chromatogram Representation of light absorbed by the sample versus time. http://purl.obolibrary.org/obo/MS_1000813 emission chromatogram http://purl.obolibrary.org/obo/MS_1000811 electromagnetic radiation chromatogram Representation of light emitted by the sample versus time. http://purl.obolibrary.org/obo/MS_1000814 counts per second http://purl.obolibrary.org/obo/MS_1000043 intensity unit The number of counted events observed per second in one or a group of elements of a detector. http://purl.obolibrary.org/obo/MS_1000815 Bruker BAF format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Bruker BAF raw file format. http://purl.obolibrary.org/obo/MS_1000816 Bruker U2 format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Bruker HyStar U2 file format. http://purl.obolibrary.org/obo/MS_1000817 HyStar http://purl.obolibrary.org/obo/MS_1000692 Bruker software Bruker software for hyphenated experiments. http://purl.obolibrary.org/obo/MS_1000818 Acquity UPLC PDA http://purl.obolibrary.org/obo/MS_1000621 photodiode array detector Acquity UPLC Photodiode Array Detector. http://purl.obolibrary.org/obo/MS_1000819 Acquity UPLC FLR http://purl.obolibrary.org/obo/MS_1002308 fluorescence detector Acquity UPLC Fluorescence Detector. http://purl.obolibrary.org/obo/MS_1000820 flow rate array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of flow rate measurements. http://purl.obolibrary.org/obo/MS_1000821 pressure array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of pressure measurements. http://purl.obolibrary.org/obo/MS_1000822 temperature array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of temperature measurements. http://purl.obolibrary.org/obo/MS_1000823 Bruker U2 nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1000824 no nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format. http://purl.obolibrary.org/obo/MS_1000825 Bruker FID format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Bruker FID file format. http://purl.obolibrary.org/obo/MS_1000826 elution time http://purl.obolibrary.org/obo/MS_1000503 scan attribute The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography. http://purl.obolibrary.org/obo/MS_1000827 isolation window target m/z http://purl.obolibrary.org/obo/MS_1000792 isolation window attribute The primary or reference m/z about which the isolation window is defined. http://purl.obolibrary.org/obo/MS_1000828 isolation window lower offset http://purl.obolibrary.org/obo/MS_1000792 isolation window attribute The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. http://purl.obolibrary.org/obo/MS_1000829 isolation window upper offset http://purl.obolibrary.org/obo/MS_1000792 isolation window attribute The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. http://purl.obolibrary.org/obo/MS_1000831 sample preparation http://purl.obolibrary.org/obo/MS_1000547 object attribute Properties of the preparation steps which took place before the measurement was performed. http://purl.obolibrary.org/obo/MS_1000834 matrix solution http://purl.obolibrary.org/obo/MS_1000832 MALDI matrix application Describes the chemical solution used as matrix. http://purl.obolibrary.org/obo/MS_1000835 matrix solution concentration http://purl.obolibrary.org/obo/MS_1000832 MALDI matrix application Concentration of the chemical solution used as matrix. http://purl.obolibrary.org/obo/MS_1000836 dried droplet MALDI matrix preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Dried droplet in MALDI matrix preparation. http://purl.obolibrary.org/obo/MS_1000837 printed MALDI matrix preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Printed MALDI matrix preparation. http://purl.obolibrary.org/obo/MS_1000838 sprayed MALDI matrix preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Sprayed MALDI matrix preparation. http://purl.obolibrary.org/obo/MS_1000839 precoated MALDI sample plate http://purl.obolibrary.org/obo/MS_1001938 sample plate type Precoated MALDI sample plate. http://purl.obolibrary.org/obo/MS_1000843 wavelength http://purl.obolibrary.org/obo/MS_1000841 laser attribute OBSOLETE The distance between two peaks of the emitted laser beam. http://purl.obolibrary.org/obo/MS_1000844 focus diameter x http://purl.obolibrary.org/obo/MS_1000841 laser attribute Describes the diameter of the laser beam in x direction. http://purl.obolibrary.org/obo/MS_1000845 focus diameter y http://purl.obolibrary.org/obo/MS_1000841 laser attribute Describes the diameter of the laser beam in y direction. http://purl.obolibrary.org/obo/MS_1000846 pulse energy http://purl.obolibrary.org/obo/MS_1000841 laser attribute Describes output energy of the laser system. May be attenuated by filters or other means. http://purl.obolibrary.org/obo/MS_1000847 pulse duration http://purl.obolibrary.org/obo/MS_1000841 laser attribute Describes how long the laser beam was emitted from the laser device. http://purl.obolibrary.org/obo/MS_1000848 attenuation http://purl.obolibrary.org/obo/MS_1000841 laser attribute Describes the reduction of the intensity of the laser beam energy. http://purl.obolibrary.org/obo/MS_1000849 impact angle http://purl.obolibrary.org/obo/MS_1000841 laser attribute Describes the angle between the laser beam and the sample target. http://purl.obolibrary.org/obo/MS_1000850 gas laser http://purl.obolibrary.org/obo/MS_1000842 laser type Laser which is powered by a gaseous medium. http://purl.obolibrary.org/obo/MS_1000851 solid-state laser http://purl.obolibrary.org/obo/MS_1000842 laser type Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states. http://purl.obolibrary.org/obo/MS_1000852 dye-laser http://purl.obolibrary.org/obo/MS_1000842 laser type Dye lasers use an organic dye as the gain medium. http://purl.obolibrary.org/obo/MS_1000853 free electron laser http://purl.obolibrary.org/obo/MS_1000842 laser type Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term. http://purl.obolibrary.org/obo/MS_1000854 LTQ XL http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Scientific LTQ XL MS. http://purl.obolibrary.org/obo/MS_1000855 LTQ Velos http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Scientific LTQ Velos MS. http://purl.obolibrary.org/obo/MS_1000856 LTQ Velos/ETD http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Scientific LTQ Velos MS with ETD. http://purl.obolibrary.org/obo/MS_1000857 run attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Properties of the described run. http://purl.obolibrary.org/obo/MS_1000858 fraction identifier http://purl.obolibrary.org/obo/MS_1000857 run attribute Identifier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information. http://purl.obolibrary.org/obo/MS_1000859 molecule http://purl.obolibrary.org/obo/MS_1000881 molecular entity Group of two or more atoms held together by chemical bonds. http://purl.obolibrary.org/obo/MS_1000860 peptide http://purl.obolibrary.org/obo/MS_1000859 molecule A molecule of low molecular weight that is composed of two or more amino acid residues. http://purl.obolibrary.org/obo/MS_1000862 isoelectric point http://purl.obolibrary.org/obo/MS_1000861 molecular entity property The pH of a solution at which a charged molecule does not migrate in an electric field. http://purl.obolibrary.org/obo/MS_1000863 predicted isoelectric point http://purl.obolibrary.org/obo/MS_1000862 isoelectric point The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm. http://purl.obolibrary.org/obo/MS_1000864 chemical formula http://purl.obolibrary.org/obo/MS_1003033 molecular entity attribute A combination of symbols used to express the chemical composition of a molecule. http://purl.obolibrary.org/obo/MS_1000865 empirical formula http://purl.obolibrary.org/obo/MS_1000864 chemical formula A chemical formula which expresses the proportions of the elements present in a substance. http://purl.obolibrary.org/obo/MS_1000866 molecular formula http://purl.obolibrary.org/obo/MS_1000864 chemical formula A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked. http://purl.obolibrary.org/obo/MS_1000867 structural formula http://purl.obolibrary.org/obo/MS_1000864 chemical formula A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other. http://purl.obolibrary.org/obo/MS_1000868 SMILES string http://purl.obolibrary.org/obo/MS_1000867 structural formula The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string. http://purl.obolibrary.org/obo/MS_1000869 collision gas pressure http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute The gas pressure of the collision gas used for collisional excitation. http://purl.obolibrary.org/obo/MS_1000870 4000 QTRAP http://purl.obolibrary.org/obo/MS_1000121 SCIEX instrument model OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000. http://purl.obolibrary.org/obo/MS_1000871 SRM software http://purl.obolibrary.org/obo/MS_1000531 software Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs. http://purl.obolibrary.org/obo/MS_1000872 MaRiMba http://purl.obolibrary.org/obo/MS_1000871 SRM software Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. http://purl.obolibrary.org/obo/MS_1000873 peptide attribute calculation software http://purl.obolibrary.org/obo/MS_1000531 software Software used to predict or calculate numerical attributes of peptides. http://purl.obolibrary.org/obo/MS_1000874 SSRCalc http://purl.obolibrary.org/obo/MS_1000873 peptide attribute calculation software Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence. http://purl.obolibrary.org/obo/MS_1000875 declustering potential http://purl.obolibrary.org/obo/MS_1000482 source attribute Potential difference between the orifice and the skimmer in volts. http://purl.obolibrary.org/obo/MS_1000876 cone voltage http://purl.obolibrary.org/obo/MS_1000482 source attribute Potential difference between the sampling cone/orifice in volts. http://purl.obolibrary.org/obo/MS_1000877 tube lens voltage http://purl.obolibrary.org/obo/MS_1000482 source attribute Potential difference setting of the tube lens in volts. http://purl.obolibrary.org/obo/MS_1000878 external reference identifier http://purl.obolibrary.org/obo/MS_1002840 external reference data An identifier/accession number to an external reference database. http://purl.obolibrary.org/obo/MS_1000879 PubMed identifier http://purl.obolibrary.org/obo/MS_1000878 external reference identifier A unique identifier for a publication in the PubMed database (MIR:00000015). http://purl.obolibrary.org/obo/MS_1000880 interchannel delay http://purl.obolibrary.org/obo/MS_1000503 scan attribute The duration of intervals between scanning, during which the instrument configuration is switched. http://purl.obolibrary.org/obo/MS_1000882 protein http://purl.obolibrary.org/obo/MS_1000859 molecule A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene. http://purl.obolibrary.org/obo/MS_1000883 protein short name http://purl.obolibrary.org/obo/MS_1000884 protein attribute A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN). http://purl.obolibrary.org/obo/MS_1000884 protein attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute A nonphysical characteristic attributed to a specific protein. http://purl.obolibrary.org/obo/MS_1000885 protein accession http://purl.obolibrary.org/obo/MS_1003046 peptide-to-protein mapping attribute Identifier for a specific protein in a database. http://purl.obolibrary.org/obo/MS_1000886 protein name http://purl.obolibrary.org/obo/MS_1000884 protein attribute A long name describing the function of the protein. http://purl.obolibrary.org/obo/MS_1000888 stripped peptide sequence http://purl.obolibrary.org/obo/MS_1003050 peptidoform attribute Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away. http://purl.obolibrary.org/obo/MS_1000889 peptidoform sequence http://purl.obolibrary.org/obo/MS_1003050 peptidoform attribute Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present. http://purl.obolibrary.org/obo/MS_1000890 peptidoform labeling state http://purl.obolibrary.org/obo/MS_1003050 peptidoform attribute A state description of how a peptide might be isotopically or isobarically labelled. http://purl.obolibrary.org/obo/MS_1000891 heavy labeled peptidoform http://purl.obolibrary.org/obo/MS_1000890 peptidoform labeling state A peptide that has been created or labelled with some heavier-than-usual isotopes. http://purl.obolibrary.org/obo/MS_1000892 unlabeled peptidoform http://purl.obolibrary.org/obo/MS_1000890 peptidoform labeling state A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy". http://purl.obolibrary.org/obo/MS_1000893 peptidoform group label http://purl.obolibrary.org/obo/MS_1003050 peptidoform attribute An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. http://purl.obolibrary.org/obo/MS_1000894 retention time http://purl.obolibrary.org/obo/MS_1003050 peptidoform attribute A time interval from the start of chromatography when an analyte exits a chromatographic column. http://purl.obolibrary.org/obo/MS_1000895 local retention time http://purl.obolibrary.org/obo/MS_1000894 retention time A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup. http://purl.obolibrary.org/obo/MS_1000896 normalized retention time http://purl.obolibrary.org/obo/MS_1003295 summary statistics of replicates A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup. http://purl.obolibrary.org/obo/MS_1000897 predicted retention time http://purl.obolibrary.org/obo/MS_1000894 retention time A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application. http://purl.obolibrary.org/obo/MS_1000899 de facto standard http://purl.obolibrary.org/obo/MS_1000898 standard A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard. http://purl.obolibrary.org/obo/MS_1000900 minimum information standard http://purl.obolibrary.org/obo/MS_1000898 standard A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result. http://purl.obolibrary.org/obo/MS_1000901 retention time normalization standard http://purl.obolibrary.org/obo/MS_1000898 standard A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column. http://purl.obolibrary.org/obo/MS_1000902 H-PINS retention time normalization standard http://purl.obolibrary.org/obo/MS_1000901 retention time normalization standard The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column. http://purl.obolibrary.org/obo/MS_1000903 product ion series ordinal http://purl.obolibrary.org/obo/MS_1001221 product ion attribute The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion). http://purl.obolibrary.org/obo/MS_1000904 product ion m/z delta http://purl.obolibrary.org/obo/MS_1001221 product ion attribute The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z. http://purl.obolibrary.org/obo/MS_1000905 percent of base peak times 100 http://purl.obolibrary.org/obo/MS_1000043 intensity unit The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries. http://purl.obolibrary.org/obo/MS_1000906 peak intensity rank http://purl.obolibrary.org/obo/MS_1000455 ion selection attribute Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc. http://purl.obolibrary.org/obo/MS_1000907 peak targeting suitability rank http://purl.obolibrary.org/obo/MS_1000455 ion selection attribute Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitable peak is 2, etc. Suitability is algorithm and context dependent. http://purl.obolibrary.org/obo/MS_1000910 transition optimized on specified instrument http://purl.obolibrary.org/obo/MS_1000909 transition validation method The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined. http://purl.obolibrary.org/obo/MS_1000911 transition validated with an MS/MS spectrum on specified instrument http://purl.obolibrary.org/obo/MS_1000909 transition validation method The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. http://purl.obolibrary.org/obo/MS_1000912 transition purported from an MS/MS spectrum on a different, specified instrument http://purl.obolibrary.org/obo/MS_1000909 transition validation method The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad). http://purl.obolibrary.org/obo/MS_1000913 transition predicted by informatic analysis http://purl.obolibrary.org/obo/MS_1000909 transition validation method The transition has been predicted by informatics software without any direct spectral evidence. http://purl.obolibrary.org/obo/MS_1000914 tab delimited text format http://purl.obolibrary.org/obo/MS_1001459 file format A file format that has two or more columns of tabular data where each column is separated by a TAB character. http://purl.obolibrary.org/obo/MS_1000916 retention time window lower offset http://purl.obolibrary.org/obo/MS_1000915 retention time window attribute The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time. http://purl.obolibrary.org/obo/MS_1000917 retention time window upper offset http://purl.obolibrary.org/obo/MS_1000915 retention time window attribute The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time. http://purl.obolibrary.org/obo/MS_1000920 includes supersede excludes http://purl.obolibrary.org/obo/MS_1000919 target inclusion exclusion priority A priority setting specifying that included targets have priority over the excluded targets if there is a conflict. http://purl.obolibrary.org/obo/MS_1000921 excludes supersede includes http://purl.obolibrary.org/obo/MS_1000919 target inclusion exclusion priority A priority setting specifying that excluded targets have priority over the included targets if there is a conflict. http://purl.obolibrary.org/obo/MS_1000922 Skyline http://purl.obolibrary.org/obo/MS_1001139 quantitation software name Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington. http://purl.obolibrary.org/obo/MS_1000923 TIQAM http://purl.obolibrary.org/obo/MS_1000871 SRM software Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology. http://purl.obolibrary.org/obo/MS_1000925 ATAQS http://purl.obolibrary.org/obo/MS_1000871 SRM software Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology. http://purl.obolibrary.org/obo/MS_1000926 product interpretation rank http://purl.obolibrary.org/obo/MS_1001221 product ion attribute The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1. http://purl.obolibrary.org/obo/MS_1000927 ion injection time http://purl.obolibrary.org/obo/MS_1000503 scan attribute The length of time spent filling an ion trapping device. http://purl.obolibrary.org/obo/MS_1000928 calibration spectrum http://purl.obolibrary.org/obo/MS_1000559 spectrum type A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample. http://purl.obolibrary.org/obo/MS_1000929 Shimadzu Biotech nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1000930 Shimadzu Biotech database entity http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Shimadzu Biotech format. http://purl.obolibrary.org/obo/MS_1000931 QTRAP 5500 http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument Applied Biosystems|MDS SCIEX QTRAP 5500. http://purl.obolibrary.org/obo/MS_1000932 TripleTOF 5600 http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1000933 protein modifications http://purl.obolibrary.org/obo/MS_1000884 protein attribute Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation. http://purl.obolibrary.org/obo/MS_1000934 gene name http://purl.obolibrary.org/obo/MS_1000884 protein attribute Name of the gene from which the protein is translated. http://purl.obolibrary.org/obo/MS_1001006 SEQUEST:ViewCV http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter SEQUEST View Input Parameters. http://purl.obolibrary.org/obo/MS_1001007 SEQUEST:OutputLines http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter Number of peptide results to show. http://purl.obolibrary.org/obo/MS_1001009 SEQUEST:DescriptionLines http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter Number of full protein descriptions to show for top N peptides. http://purl.obolibrary.org/obo/MS_1001010 de novo search http://purl.obolibrary.org/obo/MS_1001080 search type A de novo sequencing search (without database). http://purl.obolibrary.org/obo/MS_1001011 search database details http://purl.obolibrary.org/obo/MS_1001249 search input details Details about the database searched. http://purl.obolibrary.org/obo/MS_1001012 database source http://purl.obolibrary.org/obo/MS_1001011 search database details The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other). http://purl.obolibrary.org/obo/MS_1001013 database name http://purl.obolibrary.org/obo/MS_1001011 search database details The name of the search database (nr, SwissProt or est_human). http://purl.obolibrary.org/obo/MS_1001014 database local file path http://purl.obolibrary.org/obo/MS_1001011 search database details OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view. http://purl.obolibrary.org/obo/MS_1001015 database original uri http://purl.obolibrary.org/obo/MS_1001011 search database details URI, from where the search database was originally downloaded. http://purl.obolibrary.org/obo/MS_1001016 database version http://purl.obolibrary.org/obo/MS_1001011 search database details Version of the search database. In mzIdentML use the attribute instead. http://purl.obolibrary.org/obo/MS_1001017 release date http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term. http://purl.obolibrary.org/obo/MS_1001018 database type http://purl.obolibrary.org/obo/MS_1001011 search database details Database containing amino acid or nucleic acid sequences. http://purl.obolibrary.org/obo/MS_1001019 database filtering http://purl.obolibrary.org/obo/MS_1001011 search database details Was there filtering used on the database. http://purl.obolibrary.org/obo/MS_1001020 DB filter taxonomy http://purl.obolibrary.org/obo/MS_1001511 Sequence database filter types A taxonomy filter was to the database search. http://purl.obolibrary.org/obo/MS_1001021 DB filter on accession numbers http://purl.obolibrary.org/obo/MS_1001511 Sequence database filter types Filtering applied specifically by accession number pattern. http://purl.obolibrary.org/obo/MS_1001022 DB MW filter http://purl.obolibrary.org/obo/MS_1001511 Sequence database filter types Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value. http://purl.obolibrary.org/obo/MS_1001023 DB PI filter http://purl.obolibrary.org/obo/MS_1001511 Sequence database filter types Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value. http://purl.obolibrary.org/obo/MS_1001024 translation frame http://purl.obolibrary.org/obo/MS_1001011 search database details The translated open reading frames from a nucleotide database considered in the search (range: 1-6). http://purl.obolibrary.org/obo/MS_1001025 translation table http://purl.obolibrary.org/obo/MS_1001011 search database details The translation table used to translate the nucleotides to amino acids. http://purl.obolibrary.org/obo/MS_1001027 DB filter on sequence pattern http://purl.obolibrary.org/obo/MS_1001511 Sequence database filter types Filtering applied specifically by amino acid sequence pattern. http://purl.obolibrary.org/obo/MS_1001028 SEQUEST:SequenceHeaderFilter http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter String in the header of a sequence entry for that entry to be searched. http://purl.obolibrary.org/obo/MS_1001029 number of sequences searched http://purl.obolibrary.org/obo/MS_1001011 search database details The number of sequences (proteins / nucleotides) from the database search after filtering. http://purl.obolibrary.org/obo/MS_1001030 number of peptide seqs compared to each spectrum http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Number of peptide seqs compared to each spectrum. http://purl.obolibrary.org/obo/MS_1001031 spectral library search http://purl.obolibrary.org/obo/MS_1001080 search type A search using a library of spectra. http://purl.obolibrary.org/obo/MS_1001035 date / time search performed http://purl.obolibrary.org/obo/MS_1001184 search statistics OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run. http://purl.obolibrary.org/obo/MS_1001036 search time taken http://purl.obolibrary.org/obo/MS_1001184 search statistics The time taken to complete the search in seconds. http://purl.obolibrary.org/obo/MS_1001037 SEQUEST:ShowFragmentIons http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter Flag indicating that fragment ions should be shown. http://purl.obolibrary.org/obo/MS_1001038 SEQUEST:Consensus http://purl.obolibrary.org/obo/MS_1001006 SEQUEST:ViewCV Specify depth as value of the CVParam. http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format http://purl.obolibrary.org/obo/MS_1001459 file format Type of the source file, the mzIdentML was created from. http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV http://purl.obolibrary.org/obo/MS_1001006 SEQUEST:ViewCV SEQUEST View / Sort Input Parameters. http://purl.obolibrary.org/obo/MS_1001042 SEQUEST:LimitTo http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter Specify "number of dtas shown" as value of the CVParam. http://purl.obolibrary.org/obo/MS_1001044 cleavage agent details http://purl.obolibrary.org/obo/MS_1001249 search input details Details of cleavage agent (enzyme). http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name http://purl.obolibrary.org/obo/MS_1001044 cleavage agent details The name of the cleavage agent. http://purl.obolibrary.org/obo/MS_1001046 SEQUEST:sort by dCn http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results by the delta of the normalized correlation score. http://purl.obolibrary.org/obo/MS_1001047 SEQUEST:sort by dM http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M. http://purl.obolibrary.org/obo/MS_1001048 SEQUEST:sort by Ions http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the ions. http://purl.obolibrary.org/obo/MS_1001049 SEQUEST:sort by MH+ http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the mass of the protonated ion. http://purl.obolibrary.org/obo/MS_1001050 SEQUEST:sort by P http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the probability. http://purl.obolibrary.org/obo/MS_1001052 SEQUEST:sort by PreviousAminoAcid http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the previous amino acid. http://purl.obolibrary.org/obo/MS_1001053 SEQUEST:sort by Ref http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the reference. http://purl.obolibrary.org/obo/MS_1001056 modification specificity rule http://purl.obolibrary.org/obo/MS_1001055 modification parameters The specificity rules for the modifications applied by the search engine. http://purl.obolibrary.org/obo/MS_1001057 tolerance on types http://purl.obolibrary.org/obo/MS_1001055 modification parameters OBSOLETE: Tolerance on types. http://purl.obolibrary.org/obo/MS_1001058 quality estimation by manual validation http://purl.obolibrary.org/obo/MS_1001060 quality estimation method details The quality estimation was done manually. http://purl.obolibrary.org/obo/MS_1001059 SEQUEST:sort by RSp http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide). http://purl.obolibrary.org/obo/MS_1001060 quality estimation method details http://purl.obolibrary.org/obo/MS_1001249 search input details Method for quality estimation (manually or with decoy database). http://purl.obolibrary.org/obo/MS_1001061 neutral loss http://purl.obolibrary.org/obo/MS_1001055 modification parameters OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD. http://purl.obolibrary.org/obo/MS_1001062 Mascot MGF format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Mascot MGF file format. http://purl.obolibrary.org/obo/MS_1001065 TODOscoring model http://purl.obolibrary.org/obo/MS_1001249 search input details OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms. http://purl.obolibrary.org/obo/MS_1001066 ions series considered in search http://purl.obolibrary.org/obo/MS_1001249 search input details The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine. http://purl.obolibrary.org/obo/MS_1001068 SEQUEST:sort by Sp http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results by the Sp score. http://purl.obolibrary.org/obo/MS_1001069 SEQUEST:sort by TIC http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the total ion current. http://purl.obolibrary.org/obo/MS_1001070 SEQUEST:sort by Scan http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the scan number. http://purl.obolibrary.org/obo/MS_1001071 SEQUEST:sort by Sequence http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the sequence. http://purl.obolibrary.org/obo/MS_1001072 SEQUEST:sort by Sf http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the SEQUEST result 'Sf'. http://purl.obolibrary.org/obo/MS_1001073 database type amino acid http://purl.obolibrary.org/obo/MS_1001018 database type Database contains amino acid sequences. http://purl.obolibrary.org/obo/MS_1001079 database type nucleotide http://purl.obolibrary.org/obo/MS_1001018 database type Database contains nucleic acid sequences. http://purl.obolibrary.org/obo/MS_1001080 search type http://purl.obolibrary.org/obo/MS_1001249 search input details Enumeration of type of search value (i.e. from PMF, sequence tag, MS2). http://purl.obolibrary.org/obo/MS_1001081 pmf search http://purl.obolibrary.org/obo/MS_1001080 search type A peptide mass fingerprint search. http://purl.obolibrary.org/obo/MS_1001082 tag search http://purl.obolibrary.org/obo/MS_1001080 search type A sequence tag search. http://purl.obolibrary.org/obo/MS_1001083 ms-ms search http://purl.obolibrary.org/obo/MS_1001080 search type An MS2 search (with fragment ions). http://purl.obolibrary.org/obo/MS_1001084 database nr http://purl.obolibrary.org/obo/MS_1001013 database name Non-redundant GenBank sequence database. http://purl.obolibrary.org/obo/MS_1001085 protein-level identification attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Protein level information. http://purl.obolibrary.org/obo/MS_1001086 SEQUEST:sort by XCorr http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results by the correlation score. http://purl.obolibrary.org/obo/MS_1001087 SEQUEST:ProcessCV http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter SEQUEST View / Process Input Parameters. http://purl.obolibrary.org/obo/MS_1001088 protein description http://purl.obolibrary.org/obo/MS_1001342 database sequence details The protein description line from the sequence entry in the source database FASTA file. http://purl.obolibrary.org/obo/MS_1001089 molecule taxonomy http://purl.obolibrary.org/obo/MS_1001512 Sequence database filters The taxonomy of the resultant molecule from the search. http://purl.obolibrary.org/obo/MS_1001090 taxonomy nomenclature http://purl.obolibrary.org/obo/MS_1001089 molecule taxonomy OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT). http://purl.obolibrary.org/obo/MS_1001092 peptide sequence-level identification statistic http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute Identification confidence metric for a peptide. http://purl.obolibrary.org/obo/MS_1001093 sequence coverage http://purl.obolibrary.org/obo/MS_1001085 protein-level identification attribute The percent coverage for the protein based upon the matched peptide sequences (can be calculated). http://purl.obolibrary.org/obo/MS_1001094 SEQUEST:sort by z http://purl.obolibrary.org/obo/MS_1001041 SEQUEST:sortCV Sort order of SEQUEST search results given by the charge. http://purl.obolibrary.org/obo/MS_1001096 SEQUEST:TopPercentMostIntense http://purl.obolibrary.org/obo/MS_1001087 SEQUEST:ProcessCV Specify "percentage" as value of the CVParam. http://purl.obolibrary.org/obo/MS_1001097 distinct peptide sequences http://purl.obolibrary.org/obo/MS_1001085 protein-level identification attribute This counts distinct sequences hitting the protein without regard to a minimal confidence threshold. http://purl.obolibrary.org/obo/MS_1001098 confident distinct peptide sequences http://purl.obolibrary.org/obo/MS_1001085 protein-level identification attribute This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere. http://purl.obolibrary.org/obo/MS_1001099 confident peptide qualification http://purl.obolibrary.org/obo/MS_1001085 protein-level identification attribute The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than. http://purl.obolibrary.org/obo/MS_1001100 confident peptide sequence number http://purl.obolibrary.org/obo/MS_1001085 protein-level identification attribute This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere. http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship http://purl.obolibrary.org/obo/MS_1001085 protein-level identification attribute Protein group or subset relationships. http://purl.obolibrary.org/obo/MS_1001104 database UniProtKB/Swiss-Prot http://purl.obolibrary.org/obo/MS_1002126 database UniProtKB The name of the UniProtKB/Swiss-Prot knowledgebase. http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Peptide level information. http://purl.obolibrary.org/obo/MS_1001106 SEQUEST:TopNumber http://purl.obolibrary.org/obo/MS_1001087 SEQUEST:ProcessCV Specify "number" as value of the CVParam. http://purl.obolibrary.org/obo/MS_1001107 data stored in database http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was a data set in a database. http://purl.obolibrary.org/obo/MS_1001108 param: a ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: a ion with charge on the N-terminal side. http://purl.obolibrary.org/obo/MS_1001109 SEQUEST:CullTo http://purl.obolibrary.org/obo/MS_1001087 SEQUEST:ProcessCV Specify cull string as value of the CVParam. http://purl.obolibrary.org/obo/MS_1001110 SEQUEST:modeCV http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter SEQUEST Mode Input Parameters. http://purl.obolibrary.org/obo/MS_1001112 n-terminal flanking residue http://purl.obolibrary.org/obo/MS_1003046 peptide-to-protein mapping attribute Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein. http://purl.obolibrary.org/obo/MS_1001113 c-terminal flanking residue http://purl.obolibrary.org/obo/MS_1003046 peptide-to-protein mapping attribute Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein. http://purl.obolibrary.org/obo/MS_1001114 retention time(s) http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute OBSOLETE Retention time of the spectrum from the source file. http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic http://purl.obolibrary.org/obo/MS_1001085 protein-level identification attribute Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group). http://purl.obolibrary.org/obo/MS_1001117 theoretical neutral mass http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier. http://purl.obolibrary.org/obo/MS_1001118 param: b ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: b ion with charge on the N-terminal side. http://purl.obolibrary.org/obo/MS_1001119 param: c ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: c ion with charge on the N-terminal side. http://purl.obolibrary.org/obo/MS_1001121 number of matched peaks http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count. http://purl.obolibrary.org/obo/MS_1001122 ions series considered http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb). http://purl.obolibrary.org/obo/MS_1001123 number of peaks used http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't. http://purl.obolibrary.org/obo/MS_1001124 number of peaks submitted http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute The number of peaks from the original peaks listed that were submitted to the search engine. http://purl.obolibrary.org/obo/MS_1001125 manual validation http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Result of quality estimation: decision of a manual validation. http://purl.obolibrary.org/obo/MS_1001127 peptide sharing details http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute Accessions Containing Sequence - Accessions for each protein containing this peptide. http://purl.obolibrary.org/obo/MS_1001128 SEQUEST:selectCV http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter SEQUEST Select Input Parameters. http://purl.obolibrary.org/obo/MS_1001130 peptide raw area http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype OBSOLETE Peptide raw area. http://purl.obolibrary.org/obo/MS_1001131 error on peptide area http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype Error on peptide area. http://purl.obolibrary.org/obo/MS_1001132 peptide ratio http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype Peptide ratio. http://purl.obolibrary.org/obo/MS_1001133 error on peptide ratio http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype Error on peptide ratio. http://purl.obolibrary.org/obo/MS_1001134 protein ratio http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype Protein ratio. http://purl.obolibrary.org/obo/MS_1001135 error on protein ratio http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype Error on protein ratio. http://purl.obolibrary.org/obo/MS_1001136 p-value (protein diff from 1 randomly) http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype OBSOLETE P-value (protein diff from 1 randomly). http://purl.obolibrary.org/obo/MS_1001137 absolute quantity http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Absolute quantity in terms of real concentration or molecule copy number in sample. http://purl.obolibrary.org/obo/MS_1001138 error on absolute quantity http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Error on absolute quantity. http://purl.obolibrary.org/obo/MS_1001139 quantitation software name http://purl.obolibrary.org/obo/MS_1001129 quantification information Quantitation software name. http://purl.obolibrary.org/obo/MS_1001140 quantitation software version http://purl.obolibrary.org/obo/MS_1001129 quantification information OBSOLETE Quantitation software version. http://purl.obolibrary.org/obo/MS_1001141 intensity of precursor ion http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The intensity of the precursor ion. http://purl.obolibrary.org/obo/MS_1001142 database IPI_human http://purl.obolibrary.org/obo/MS_1001013 database name International Protein Index database for Homo sapiens sequences. http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic http://purl.obolibrary.org/obo/MS_1002347 PSM-level identification statistic Search engine specific peptide spectrum match scores. http://purl.obolibrary.org/obo/MS_1001145 SEQUEST:SelectAdvancedCV http://purl.obolibrary.org/obo/MS_1001128 SEQUEST:selectCV SEQUEST Select Advanced Input Parameters. http://purl.obolibrary.org/obo/MS_1001146 param: a ion-NH3 DEPRECATED http://purl.obolibrary.org/obo/MS_1001066 ions series considered in search Ion a-NH3 parameter information, type of product: a ion with lost ammonia. http://purl.obolibrary.org/obo/MS_1001148 param: a ion-H2O DEPRECATED http://purl.obolibrary.org/obo/MS_1001066 ions series considered in search Ion a-H2O if a significant and fragment includes STED. http://purl.obolibrary.org/obo/MS_1001149 param: b ion-NH3 DEPRECATED http://purl.obolibrary.org/obo/MS_1001066 ions series considered in search Ion b-NH3 parameter information, type of product: b ion with lost ammonia. http://purl.obolibrary.org/obo/MS_1001150 param: b ion-H2O DEPRECATED http://purl.obolibrary.org/obo/MS_1001066 ions series considered in search Ion b-H2O if b significant and fragment includes STED. http://purl.obolibrary.org/obo/MS_1001151 param: y ion-NH3 DEPRECATED http://purl.obolibrary.org/obo/MS_1001066 ions series considered in search Ion y-NH3 parameter information, type of product: y ion with lost ammonia. http://purl.obolibrary.org/obo/MS_1001153 search engine specific score http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Search engine specific scores. http://purl.obolibrary.org/obo/MS_1001154 SEQUEST:probability http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'Probability'. http://purl.obolibrary.org/obo/MS_1001155 SEQUEST:xcorr http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'XCorr'. http://purl.obolibrary.org/obo/MS_1001156 SEQUEST:deltacn http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'DeltaCn'. http://purl.obolibrary.org/obo/MS_1001157 SEQUEST:sp http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The SEQUEST result 'Sp' (protein). http://purl.obolibrary.org/obo/MS_1001159 SEQUEST:expectation value http://purl.obolibrary.org/obo/MS_1001153 search engine specific score The SEQUEST result 'Expectation value'. http://purl.obolibrary.org/obo/MS_1001160 SEQUEST:sf http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'Sf'. http://purl.obolibrary.org/obo/MS_1001161 SEQUEST:matched ions http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'Matched Ions'. http://purl.obolibrary.org/obo/MS_1001162 SEQUEST:total ions http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'Total Ions'. http://purl.obolibrary.org/obo/MS_1001163 SEQUEST:consensus score http://purl.obolibrary.org/obo/MS_1001153 search engine specific score The SEQUEST result 'Consensus Score'. http://purl.obolibrary.org/obo/MS_1001164 Paragon:unused protscore http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups The Paragon result 'Unused ProtScore'. http://purl.obolibrary.org/obo/MS_1001165 Paragon:total protscore http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups The Paragon result 'Total ProtScore'. http://purl.obolibrary.org/obo/MS_1001166 Paragon:score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The Paragon result 'Score'. http://purl.obolibrary.org/obo/MS_1001167 Paragon:confidence http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The Paragon result 'Confidence'. http://purl.obolibrary.org/obo/MS_1001168 Paragon:expression error factor http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The Paragon result 'Expression Error Factor'. http://purl.obolibrary.org/obo/MS_1001169 Paragon:expression change p-value http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The Paragon result 'Expression change P-value'. http://purl.obolibrary.org/obo/MS_1001170 Paragon:contrib http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The Paragon result 'Contrib'. http://purl.obolibrary.org/obo/MS_1001171 Mascot:score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Mascot result 'Score'. http://purl.obolibrary.org/obo/MS_1001172 Mascot:expectation value http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Mascot result 'expectation value'. http://purl.obolibrary.org/obo/MS_1001173 Mascot:matched ions http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Mascot result 'Matched ions'. http://purl.obolibrary.org/obo/MS_1001174 Mascot:total ions http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Mascot result 'Total ions'. http://purl.obolibrary.org/obo/MS_1001175 peptide shared in multiple proteins http://purl.obolibrary.org/obo/MS_1001127 peptide sharing details A peptide matching multiple proteins. http://purl.obolibrary.org/obo/MS_1001176 (?<=[KR])(?!P) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for Trypsin. http://purl.obolibrary.org/obo/MS_1001177 number of molecular hypothesis considered http://purl.obolibrary.org/obo/MS_1001184 search statistics Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search. http://purl.obolibrary.org/obo/MS_1001178 database EST http://purl.obolibrary.org/obo/MS_1001079 database type nucleotide Expressed sequence tag nucleotide sequence database. http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression http://purl.obolibrary.org/obo/MS_1002479 regular expression Regular expressions for cleavage enzymes. http://purl.obolibrary.org/obo/MS_1001184 search statistics http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details The details of the actual run of the search. http://purl.obolibrary.org/obo/MS_1001189 modification specificity peptide N-term http://purl.obolibrary.org/obo/MS_1001056 modification specificity rule As parameter for search engine: apply the modification only at the N-terminus of a peptide. http://purl.obolibrary.org/obo/MS_1001190 modification specificity peptide C-term http://purl.obolibrary.org/obo/MS_1001056 modification specificity rule As parameter for search engine: apply the modification only at the C-terminus of a peptide. http://purl.obolibrary.org/obo/MS_1001191 p-value http://purl.obolibrary.org/obo/MS_1001198 protein identification confidence metric OBSOLETE Quality estimation by p-value. http://purl.obolibrary.org/obo/MS_1001192 Expect value http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Result of quality estimation: Expect value. http://purl.obolibrary.org/obo/MS_1001193 confidence score http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Result of quality estimation: confidence score. http://purl.obolibrary.org/obo/MS_1001194 quality estimation with decoy database http://purl.obolibrary.org/obo/MS_1001060 quality estimation method details Quality estimation by decoy database. http://purl.obolibrary.org/obo/MS_1001195 decoy DB type reverse http://purl.obolibrary.org/obo/MS_1001450 decoy DB details Decoy type: Amino acids of protein sequences are used in reverse order. http://purl.obolibrary.org/obo/MS_1001196 decoy DB type randomized http://purl.obolibrary.org/obo/MS_1001450 decoy DB details Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass). http://purl.obolibrary.org/obo/MS_1001197 DB composition target+decoy http://purl.obolibrary.org/obo/MS_1001450 decoy DB details Decoy database composition: database contains original (target) and decoy entries. http://purl.obolibrary.org/obo/MS_1001198 protein identification confidence metric http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Identification confidence metric for a protein. http://purl.obolibrary.org/obo/MS_1001199 Mascot DAT format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in Mascot DAT file format. http://purl.obolibrary.org/obo/MS_1001200 SEQUEST out file format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in SEQUEST out file format. http://purl.obolibrary.org/obo/MS_1001201 DB MW filter maximum http://purl.obolibrary.org/obo/MS_1001512 Sequence database filters Maximum value of molecular weight filter. http://purl.obolibrary.org/obo/MS_1001202 DB MW filter minimum http://purl.obolibrary.org/obo/MS_1001512 Sequence database filters Minimum value of molecular weight filter. http://purl.obolibrary.org/obo/MS_1001203 DB PI filter maximum http://purl.obolibrary.org/obo/MS_1001512 Sequence database filters Maximum value of isoelectric point filter. http://purl.obolibrary.org/obo/MS_1001204 DB PI filter minimum http://purl.obolibrary.org/obo/MS_1001512 Sequence database filters Minimum value of isoelectric point filter. http://purl.obolibrary.org/obo/MS_1001207 Mascot http://purl.obolibrary.org/obo/MS_1001456 analysis software The name of the Mascot search engine. http://purl.obolibrary.org/obo/MS_1001208 SEQUEST http://purl.obolibrary.org/obo/MS_1001456 analysis software The name of the SEQUEST search engine. http://purl.obolibrary.org/obo/MS_1001209 Phenyx http://purl.obolibrary.org/obo/MS_1001456 analysis software The name of the Phenyx search engine. http://purl.obolibrary.org/obo/MS_1001210 mass type settings http://purl.obolibrary.org/obo/MS_1001249 search input details The type of mass difference value to be considered by the search engine (monoisotopic or average). http://purl.obolibrary.org/obo/MS_1001211 parent mass type mono http://purl.obolibrary.org/obo/MS_1001210 mass type settings Mass type setting for parent mass was monoisotopic. http://purl.obolibrary.org/obo/MS_1001212 parent mass type average http://purl.obolibrary.org/obo/MS_1001210 mass type settings Mass type setting for parent mass was average isotopic. http://purl.obolibrary.org/obo/MS_1001214 protein-level global FDR http://purl.obolibrary.org/obo/MS_1002705 protein-level result list statistic Estimation of the global false discovery rate of proteins. http://purl.obolibrary.org/obo/MS_1001215 SEQUEST:PeptideSp http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'Sp' in out file (peptide). http://purl.obolibrary.org/obo/MS_1001217 SEQUEST:PeptideRankSp http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'. http://purl.obolibrary.org/obo/MS_1001218 SEQUEST:PeptideNumber http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result '#' in out file (peptide). http://purl.obolibrary.org/obo/MS_1001219 SEQUEST:PeptideIdnumber http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'Id#' in out file (peptide). http://purl.obolibrary.org/obo/MS_1001220 frag: y ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: y ion. http://purl.obolibrary.org/obo/MS_1001221 product ion attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Fragmentation information like ion types. http://purl.obolibrary.org/obo/MS_1001222 frag: b ion - H2O http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: b ion without water. http://purl.obolibrary.org/obo/MS_1001223 frag: y ion - H2O http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: y ion without water. http://purl.obolibrary.org/obo/MS_1001224 frag: b ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: b ion. http://purl.obolibrary.org/obo/MS_1001225 product ion m/z http://purl.obolibrary.org/obo/MS_1001221 product ion attribute The m/z of the product ion. http://purl.obolibrary.org/obo/MS_1001226 product ion intensity http://purl.obolibrary.org/obo/MS_1001221 product ion attribute The intensity of a single product ion. http://purl.obolibrary.org/obo/MS_1001227 product ion m/z error http://purl.obolibrary.org/obo/MS_1001221 product ion attribute The product ion m/z error. http://purl.obolibrary.org/obo/MS_1001228 frag: x ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: x ion. http://purl.obolibrary.org/obo/MS_1001229 frag: a ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: a ion. http://purl.obolibrary.org/obo/MS_1001230 frag: z ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: z ion. http://purl.obolibrary.org/obo/MS_1001231 frag: c ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: c ion. http://purl.obolibrary.org/obo/MS_1001232 frag: b ion - NH3 http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Ion b-NH3 fragmentation information, type of product: b ion without ammonia. http://purl.obolibrary.org/obo/MS_1001233 frag: y ion - NH3 http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Ion y-NH3 fragmentation information, type of product: y ion without ammonia. http://purl.obolibrary.org/obo/MS_1001234 frag: a ion - H2O http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: a ion without water. http://purl.obolibrary.org/obo/MS_1001235 frag: a ion - NH3 http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Ion a-NH3 fragmentation information, type of product: a ion without ammonia. http://purl.obolibrary.org/obo/MS_1001236 frag: d ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: d ion. http://purl.obolibrary.org/obo/MS_1001237 frag: v ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: v ion. http://purl.obolibrary.org/obo/MS_1001238 frag: w ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: w ion. http://purl.obolibrary.org/obo/MS_1001239 frag: immonium ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: immonium ion. http://purl.obolibrary.org/obo/MS_1001240 non-identified ion http://purl.obolibrary.org/obo/MS_1001221 product ion attribute Non-identified ion. http://purl.obolibrary.org/obo/MS_1001241 co-eluting ion http://purl.obolibrary.org/obo/MS_1001221 product ion attribute Co-eluting ion. http://purl.obolibrary.org/obo/MS_1001242 SEQUEST out folder http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was a SEQUEST folder with its out files. http://purl.obolibrary.org/obo/MS_1001243 SEQUEST summary http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was a SEQUEST summary page (proteins). http://purl.obolibrary.org/obo/MS_1001245 PerSeptive PKS format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format PerSeptive peak list file format. http://purl.obolibrary.org/obo/MS_1001246 SCIEX API III format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format PE SCIEX peak list file format. http://purl.obolibrary.org/obo/MS_1001247 Bruker XML format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Bruker data exchange XML format. http://purl.obolibrary.org/obo/MS_1001250 local FDR http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Result of quality estimation: the local FDR at the current position of a sorted list. http://purl.obolibrary.org/obo/MS_1001251 Trypsin http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Enzyme trypsin. http://purl.obolibrary.org/obo/MS_1001252 DB source EBI http://purl.obolibrary.org/obo/MS_1001012 database source Database source EBI. http://purl.obolibrary.org/obo/MS_1001253 DB source NCBI http://purl.obolibrary.org/obo/MS_1001012 database source Database source NCBI. http://purl.obolibrary.org/obo/MS_1001254 DB source UniProt http://purl.obolibrary.org/obo/MS_1001012 database source Database source UniProt. http://purl.obolibrary.org/obo/MS_1001255 fragment mass type average http://purl.obolibrary.org/obo/MS_1001210 mass type settings Mass type setting for fragment mass was average isotopic. http://purl.obolibrary.org/obo/MS_1001256 fragment mass type mono http://purl.obolibrary.org/obo/MS_1001210 mass type settings Mass type setting for fragment mass was monoisotopic. http://purl.obolibrary.org/obo/MS_1001257 param: v ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: side chain loss v ion. http://purl.obolibrary.org/obo/MS_1001258 param: d ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: side chain loss d ion. http://purl.obolibrary.org/obo/MS_1001259 param: immonium ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: immonium ion. http://purl.obolibrary.org/obo/MS_1001260 param: w ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: side chain loss w ion. http://purl.obolibrary.org/obo/MS_1001261 param: x ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: x ion with charge on the C-terminal side. http://purl.obolibrary.org/obo/MS_1001262 param: y ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: y ion with charge on the C-terminal side. http://purl.obolibrary.org/obo/MS_1001263 param: z ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: z ion with charge on the C-terminal side. http://purl.obolibrary.org/obo/MS_1001266 role type http://purl.obolibrary.org/obo/MS_1000585 contact attribute Role of a Person or Organization. http://purl.obolibrary.org/obo/MS_1001267 software vendor http://purl.obolibrary.org/obo/MS_1001266 role type Software vendor role. http://purl.obolibrary.org/obo/MS_1001268 programmer http://purl.obolibrary.org/obo/MS_1001266 role type Programmer role. http://purl.obolibrary.org/obo/MS_1001269 instrument vendor http://purl.obolibrary.org/obo/MS_1001266 role type Instrument vendor role. http://purl.obolibrary.org/obo/MS_1001270 lab personnel http://purl.obolibrary.org/obo/MS_1001266 role type Lab personnel role. http://purl.obolibrary.org/obo/MS_1001271 researcher http://purl.obolibrary.org/obo/MS_1001266 role type Researcher role. http://purl.obolibrary.org/obo/MS_1001272 (?<=R)(?!P) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for Arg-C. http://purl.obolibrary.org/obo/MS_1001273 (?=[BD]) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for Asp-N. http://purl.obolibrary.org/obo/MS_1001274 (?=[DE]) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for Asp-N-ambic. http://purl.obolibrary.org/obo/MS_1001275 ProteinScape SearchEvent http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source data for this mzIdentML was a ProteinScape SearchEvent. http://purl.obolibrary.org/obo/MS_1001276 ProteinScape Gel http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source data for this mzIdentML was a ProteinScape Gel. http://purl.obolibrary.org/obo/MS_1001283 decoy DB accession regexp http://purl.obolibrary.org/obo/MS_1001450 decoy DB details Specify the regular expression for decoy accession numbers. http://purl.obolibrary.org/obo/MS_1001284 decoy DB derived from http://purl.obolibrary.org/obo/MS_1001450 decoy DB details OBSOLETE The name of the database, the search database was derived from. http://purl.obolibrary.org/obo/MS_1001285 database IPI_mouse http://purl.obolibrary.org/obo/MS_1001013 database name International Protein Index database for Mus musculus sequences. http://purl.obolibrary.org/obo/MS_1001286 database IPI_rat http://purl.obolibrary.org/obo/MS_1001013 database name International Protein Index database for Rattus norvegicus sequences. http://purl.obolibrary.org/obo/MS_1001287 database IPI_zebrafish http://purl.obolibrary.org/obo/MS_1001013 database name International Protein Index database for Danio rerio sequences. http://purl.obolibrary.org/obo/MS_1001288 database IPI_chicken http://purl.obolibrary.org/obo/MS_1001013 database name International Protein Index database for Gallus gallus sequences. http://purl.obolibrary.org/obo/MS_1001289 database IPI_cow http://purl.obolibrary.org/obo/MS_1001013 database name International Protein Index database for Bos taurus sequences. http://purl.obolibrary.org/obo/MS_1001290 database IPI_arabidopsis http://purl.obolibrary.org/obo/MS_1001013 database name International Protein Index database for Arabidopsis thaliana sequences. http://purl.obolibrary.org/obo/MS_1001301 protein rank http://purl.obolibrary.org/obo/MS_1001085 protein-level identification attribute The rank of the protein in a list sorted by the search engine. http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter http://purl.obolibrary.org/obo/MS_1002093 search engine input parameter Search engine specific input parameters. http://purl.obolibrary.org/obo/MS_1001303 Arg-C http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Endoproteinase Arg-C. http://purl.obolibrary.org/obo/MS_1001304 Asp-N http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Endoproteinase Asp-N. http://purl.obolibrary.org/obo/MS_1001305 Asp-N_ambic http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Enzyme Asp-N, Ammonium Bicarbonate (AmBic). http://purl.obolibrary.org/obo/MS_1001306 Chymotrypsin http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Enzyme chymotrypsin. http://purl.obolibrary.org/obo/MS_1001307 CNBr http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Cyanogen bromide. http://purl.obolibrary.org/obo/MS_1001308 Formic_acid http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Formic acid. http://purl.obolibrary.org/obo/MS_1001309 Lys-C http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Endoproteinase Lys-C. http://purl.obolibrary.org/obo/MS_1001310 Lys-C/P http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Proteinase Lys-C/P. http://purl.obolibrary.org/obo/MS_1001311 PepsinA http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name PepsinA proteinase. http://purl.obolibrary.org/obo/MS_1001312 TrypChymo http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Cleavage agent TrypChymo. http://purl.obolibrary.org/obo/MS_1001313 Trypsin/P http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Cleavage agent Trypsin/P. http://purl.obolibrary.org/obo/MS_1001314 V8-DE http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Cleavage agent V8-DE. http://purl.obolibrary.org/obo/MS_1001315 V8-E http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Cleavage agent V8-E. http://purl.obolibrary.org/obo/MS_1001316 Mascot:SigThreshold http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05). http://purl.obolibrary.org/obo/MS_1001317 Mascot:MaxProteinHits http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1. http://purl.obolibrary.org/obo/MS_1001318 Mascot:ProteinScoringMethod http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter Mascot protein scoring method; either 'Standard' or 'MudPIT'. http://purl.obolibrary.org/obo/MS_1001319 Mascot:MinMSMSThreshold http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed. http://purl.obolibrary.org/obo/MS_1001320 Mascot:ShowHomologousProteinsWithSamePeptides http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed. http://purl.obolibrary.org/obo/MS_1001321 Mascot:ShowHomologousProteinsWithSubsetOfPeptides http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed. http://purl.obolibrary.org/obo/MS_1001322 Mascot:RequireBoldRed http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits. http://purl.obolibrary.org/obo/MS_1001323 Mascot:UseUnigeneClustering http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use. http://purl.obolibrary.org/obo/MS_1001324 Mascot:IncludeErrorTolerantMatches http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included. http://purl.obolibrary.org/obo/MS_1001325 Mascot:ShowDecoyMatches http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database. http://purl.obolibrary.org/obo/MS_1001328 OMSSA:evalue http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic OMSSA E-value. http://purl.obolibrary.org/obo/MS_1001329 OMSSA:pvalue http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic OMSSA p-value. http://purl.obolibrary.org/obo/MS_1001330 X!Tandem:expect http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The X!Tandem expectation value. http://purl.obolibrary.org/obo/MS_1001331 X!Tandem:hyperscore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The X!Tandem hyperscore. http://purl.obolibrary.org/obo/MS_1001332 (?<=[FYWL])(?!P) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for Chymotrypsin. http://purl.obolibrary.org/obo/MS_1001333 (?<=M) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for CNBr. http://purl.obolibrary.org/obo/MS_1001334 ((?<=D))|((?=D)) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for formic acid. http://purl.obolibrary.org/obo/MS_1001335 (?<=K)(?!P) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for Lys-C. http://purl.obolibrary.org/obo/MS_1001336 (?<=K) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for Lys-C/P. http://purl.obolibrary.org/obo/MS_1001337 (?<=[FL]) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for PepsinA. http://purl.obolibrary.org/obo/MS_1001338 (?<=[FYWLKR])(?!P) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for TrypChymo. http://purl.obolibrary.org/obo/MS_1001339 (?<=[KR]) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for Trypsin/P. http://purl.obolibrary.org/obo/MS_1001340 (?<=[BDEZ])(?!P) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for V8-DE. http://purl.obolibrary.org/obo/MS_1001341 (?<=[EZ])(?!P) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for V8-E. http://purl.obolibrary.org/obo/MS_1001342 database sequence details http://purl.obolibrary.org/obo/MS_1001011 search database details Details about a single database sequence. http://purl.obolibrary.org/obo/MS_1001343 NA sequence http://purl.obolibrary.org/obo/MS_1001342 database sequence details The sequence is a nucleic acid sequence. http://purl.obolibrary.org/obo/MS_1001344 AA sequence http://purl.obolibrary.org/obo/MS_1001342 database sequence details The sequence is a amino acid sequence. http://purl.obolibrary.org/obo/MS_1001345 mass table source http://purl.obolibrary.org/obo/MS_1001354 mass table options Children of this term specify the source of the mass table used. http://purl.obolibrary.org/obo/MS_1001346 AAIndex mass table http://purl.obolibrary.org/obo/MS_1001345 mass table source The masses used in the mass table are taken from AAIndex. http://purl.obolibrary.org/obo/MS_1001347 database file formats http://purl.obolibrary.org/obo/MS_1001011 search database details The children of this term define file formats of the sequence database used. http://purl.obolibrary.org/obo/MS_1001348 FASTA format http://purl.obolibrary.org/obo/MS_1001347 database file formats The sequence database was stored in the FASTA format. http://purl.obolibrary.org/obo/MS_1001349 ASN.1 http://purl.obolibrary.org/obo/MS_1001347 database file formats The sequence database was stored in the Abstract Syntax Notation 1 format. http://purl.obolibrary.org/obo/MS_1001350 NCBI *.p* http://purl.obolibrary.org/obo/MS_1001347 database file formats The sequence database was stored in the NCBI formatdb (*.p*) format. http://purl.obolibrary.org/obo/MS_1001351 clustal aln http://purl.obolibrary.org/obo/MS_1001347 database file formats ClustalW ALN (multiple alignment) format. http://purl.obolibrary.org/obo/MS_1001352 embl em http://purl.obolibrary.org/obo/MS_1001347 database file formats EMBL entry format. http://purl.obolibrary.org/obo/MS_1001353 NBRF PIR http://purl.obolibrary.org/obo/MS_1001347 database file formats The NBRF PIR was used as format. http://purl.obolibrary.org/obo/MS_1001355 peptide descriptions http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute Descriptions of peptides. http://purl.obolibrary.org/obo/MS_1001356 spectrum descriptions http://purl.obolibrary.org/obo/MS_1001249 search input details Descriptions of the input spectra. http://purl.obolibrary.org/obo/MS_1001357 spectrum quality descriptions http://purl.obolibrary.org/obo/MS_1001356 spectrum descriptions Description of the quality of the input spectrum. http://purl.obolibrary.org/obo/MS_1001358 msmsEval quality http://purl.obolibrary.org/obo/MS_1001357 spectrum quality descriptions This term reports the quality of the spectrum assigned by msmsEval. http://purl.obolibrary.org/obo/MS_1001360 alternate single letter codes http://purl.obolibrary.org/obo/MS_1001359 ambiguous residues List of standard residue one letter codes which are used to replace a non-standard. http://purl.obolibrary.org/obo/MS_1001361 alternate mass http://purl.obolibrary.org/obo/MS_1001359 ambiguous residues List of masses a non-standard letter code is replaced with. http://purl.obolibrary.org/obo/MS_1001362 number of unmatched peaks http://purl.obolibrary.org/obo/MS_1002345 PSM-level attribute The number of unmatched peaks. http://purl.obolibrary.org/obo/MS_1001363 peptide unique to one protein http://purl.obolibrary.org/obo/MS_1001127 peptide sharing details A peptide matching only one. http://purl.obolibrary.org/obo/MS_1001364 peptide sequence-level global FDR http://purl.obolibrary.org/obo/MS_1002703 peptide sequence-level result list statistic Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). http://purl.obolibrary.org/obo/MS_1001365 frag: internal yb ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: internal yb ion. http://purl.obolibrary.org/obo/MS_1001366 frag: internal ya ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: internal ya ion. http://purl.obolibrary.org/obo/MS_1001367 frag: z+1 ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: z+1 ion. http://purl.obolibrary.org/obo/MS_1001368 frag: z+2 ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: z+2 ion. http://purl.obolibrary.org/obo/MS_1001369 text format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Simple text file format of "m/z [intensity]" values for a PMF (or single MS2) search. http://purl.obolibrary.org/obo/MS_1001370 Mascot:homology threshold http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Mascot result 'homology threshold'. http://purl.obolibrary.org/obo/MS_1001371 Mascot:identity threshold http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Mascot result 'identity threshold'. http://purl.obolibrary.org/obo/MS_1001373 SEQUEST:TIC http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins SEQUEST total ion current. http://purl.obolibrary.org/obo/MS_1001375 Phenyx:Instrument Type http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The instrument type parameter value in Phenyx. http://purl.obolibrary.org/obo/MS_1001376 Phenyx:Scoring Model http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The selected scoring model in Phenyx. http://purl.obolibrary.org/obo/MS_1001377 Phenyx:Default Parent Charge http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The default parent charge value in Phenyx. http://purl.obolibrary.org/obo/MS_1001378 Phenyx:Trust Parent Charge http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct. http://purl.obolibrary.org/obo/MS_1001379 Phenyx:Turbo http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The turbo mode parameter in Phenyx. http://purl.obolibrary.org/obo/MS_1001380 Phenyx:Turbo:ErrorTol http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx. http://purl.obolibrary.org/obo/MS_1001381 Phenyx:Turbo:Coverage http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx. http://purl.obolibrary.org/obo/MS_1001382 Phenyx:Turbo:Series http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The list of ion series considered in the turbo mode of Phenyx. http://purl.obolibrary.org/obo/MS_1001383 Phenyx:MinPepLength http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The minimal number of residues for a peptide to be considered for a valid identification in Phenyx. http://purl.obolibrary.org/obo/MS_1001384 Phenyx:MinPepzscore http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx. http://purl.obolibrary.org/obo/MS_1001385 Phenyx:MaxPepPvalue http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx. http://purl.obolibrary.org/obo/MS_1001386 Phenyx:AC Score http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx. http://purl.obolibrary.org/obo/MS_1001387 Phenyx:Conflict Resolution http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used. http://purl.obolibrary.org/obo/MS_1001388 Phenyx:AC http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The primary sequence database identifier of a protein in Phenyx. http://purl.obolibrary.org/obo/MS_1001389 Phenyx:ID http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins A secondary sequence database identifier of a protein in Phenyx. http://purl.obolibrary.org/obo/MS_1001390 Phenyx:Score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The protein score of a protein match in Phenyx. http://purl.obolibrary.org/obo/MS_1001391 Phenyx:Peptides1 http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins First number of phenyx result "#Peptides". http://purl.obolibrary.org/obo/MS_1001392 Phenyx:Peptides2 http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins Second number of phenyx result "#Peptides". http://purl.obolibrary.org/obo/MS_1001393 Phenyx:Auto http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The value of the automatic peptide acceptance filter in Phenyx. http://purl.obolibrary.org/obo/MS_1001394 Phenyx:User http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The value of the user-defined peptide acceptance filter in Phenyx. http://purl.obolibrary.org/obo/MS_1001395 Phenyx:Pepzscore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The z-score value of a peptide sequence match in Phenyx. http://purl.obolibrary.org/obo/MS_1001396 Phenyx:PepPvalue http://purl.obolibrary.org/obo/MS_1002358 search engine specific peptide sequence-level identification statistic The p-value of a peptide sequence match in Phenyx. http://purl.obolibrary.org/obo/MS_1001397 Phenyx:NumberOfMC http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The number of missed cleavages of a peptide sequence in Phenyx. http://purl.obolibrary.org/obo/MS_1001398 Phenyx:Modif http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx. http://purl.obolibrary.org/obo/MS_1001399 OMSSA csv format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in OMSSA csv file format. http://purl.obolibrary.org/obo/MS_1001400 OMSSA xml format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in OMSSA xml file format. http://purl.obolibrary.org/obo/MS_1001401 X!Tandem xml format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in X!Tandem xml file format. http://purl.obolibrary.org/obo/MS_1001406 param: internal yb ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: internal yb ion. http://purl.obolibrary.org/obo/MS_1001407 param: internal ya ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: internal ya ion. http://purl.obolibrary.org/obo/MS_1001408 param: z+1 ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: z+1 ion. http://purl.obolibrary.org/obo/MS_1001409 param: z+2 ion http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search Parameter information, type of product: z+2 ion. http://purl.obolibrary.org/obo/MS_1001410 translation start codons http://purl.obolibrary.org/obo/MS_1001011 search database details The translation start codons used to translate the nucleotides to amino acids. http://purl.obolibrary.org/obo/MS_1001411 search tolerance specification http://purl.obolibrary.org/obo/MS_1001249 search input details Specification of the search tolerance. http://purl.obolibrary.org/obo/MS_1001414 MGF scans http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file. http://purl.obolibrary.org/obo/MS_1001415 MGF raw scans http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file. http://purl.obolibrary.org/obo/MS_1001416 spectrum title http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE. http://purl.obolibrary.org/obo/MS_1001417 SpectraST:dot http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic SpectraST dot product of two spectra, measuring spectral similarity. http://purl.obolibrary.org/obo/MS_1001418 SpectraST:dot_bias http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic SpectraST measure of how much of the dot product is dominated by a few peaks. http://purl.obolibrary.org/obo/MS_1001419 SpectraST:discriminant score F http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic SpectraST spectrum score. http://purl.obolibrary.org/obo/MS_1001420 SpectraST:delta http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic SpectraST normalised difference between dot product of top hit and runner-up. http://purl.obolibrary.org/obo/MS_1001421 pepXML format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers. http://purl.obolibrary.org/obo/MS_1001422 protXML format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers. http://purl.obolibrary.org/obo/MS_1001423 translation table description http://purl.obolibrary.org/obo/MS_1001011 search database details A URL that describes the translation table used to translate the nucleotides to amino acids. http://purl.obolibrary.org/obo/MS_1001424 ProteinExtractor:Methodname http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Name of the used method in the ProteinExtractor algorithm. http://purl.obolibrary.org/obo/MS_1001425 ProteinExtractor:GenerateNonRedundant http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Flag indicating if a non redundant scoring should be generated. http://purl.obolibrary.org/obo/MS_1001426 ProteinExtractor:IncludeIdentified http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Flag indicating if identified proteins should be included. http://purl.obolibrary.org/obo/MS_1001427 ProteinExtractor:MaxNumberOfProteins http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter The maximum number of proteins to consider. http://purl.obolibrary.org/obo/MS_1001428 ProteinExtractor:MaxProteinMass http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter The maximum considered mass for a protein. http://purl.obolibrary.org/obo/MS_1001429 ProteinExtractor:MinNumberOfPeptides http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter The minimum number of proteins to consider. http://purl.obolibrary.org/obo/MS_1001430 ProteinExtractor:UseMascot http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score. http://purl.obolibrary.org/obo/MS_1001431 ProteinExtractor:MascotPeptideScoreThreshold http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score. http://purl.obolibrary.org/obo/MS_1001432 ProteinExtractor:MascotUniqueScore http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation. http://purl.obolibrary.org/obo/MS_1001434 ProteinExtractor:MascotWeighting http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. http://purl.obolibrary.org/obo/MS_1001435 ProteinExtractor:UseSequest http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score. http://purl.obolibrary.org/obo/MS_1001436 ProteinExtractor:SequestPeptideScoreThreshold http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score. http://purl.obolibrary.org/obo/MS_1001437 ProteinExtractor:SequestUniqueScore http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation. http://purl.obolibrary.org/obo/MS_1001438 ProteinExtractor:SequestWeighting http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. http://purl.obolibrary.org/obo/MS_1001439 ProteinExtractor:UseProteinSolver http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score. http://purl.obolibrary.org/obo/MS_1001440 ProteinExtractor:ProteinSolverPeptideScoreThreshold http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score. http://purl.obolibrary.org/obo/MS_1001441 ProteinExtractor:ProteinSolverUniqueScore http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation. http://purl.obolibrary.org/obo/MS_1001442 ProteinExtractor:ProteinSolverWeighting http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. http://purl.obolibrary.org/obo/MS_1001443 ProteinExtractor:UsePhenyx http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score. http://purl.obolibrary.org/obo/MS_1001444 ProteinExtractor:PhenyxPeptideScoreThreshold http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score. http://purl.obolibrary.org/obo/MS_1001445 ProteinExtractor:PhenyxUniqueScore http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation. http://purl.obolibrary.org/obo/MS_1001446 ProteinExtractor:PhenyxWeighting http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. http://purl.obolibrary.org/obo/MS_1001447 prot:FDR threshold http://purl.obolibrary.org/obo/MS_1002485 protein-level statistical threshold False-discovery rate threshold for proteins. http://purl.obolibrary.org/obo/MS_1001448 pep:FDR threshold http://purl.obolibrary.org/obo/MS_1002484 peptide-level statistical threshold False-discovery rate threshold for peptides. http://purl.obolibrary.org/obo/MS_1001449 OMSSA e-value threshold http://purl.obolibrary.org/obo/MS_1002099 OMSSA input parameter Threshold for OMSSA e-value for quality estimation. http://purl.obolibrary.org/obo/MS_1001450 decoy DB details http://purl.obolibrary.org/obo/MS_1001011 search database details Details of decoy generation and database structure. http://purl.obolibrary.org/obo/MS_1001451 decoy DB generation algorithm http://purl.obolibrary.org/obo/MS_1001450 decoy DB details Name of algorithm used for decoy generation. http://purl.obolibrary.org/obo/MS_1001452 decoy DB type shuffle http://purl.obolibrary.org/obo/MS_1001450 decoy DB details Decoy type: Amino acids of protein sequences are used in a random order. http://purl.obolibrary.org/obo/MS_1001453 DB composition only decoy http://purl.obolibrary.org/obo/MS_1001450 decoy DB details Decoy database composition: database contains only decoy entries. http://purl.obolibrary.org/obo/MS_1001454 quality estimation with implicit decoy sequences http://purl.obolibrary.org/obo/MS_1001060 quality estimation method details Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy). http://purl.obolibrary.org/obo/MS_1001455 acquisition software http://purl.obolibrary.org/obo/MS_1000531 software Acquisition software. http://purl.obolibrary.org/obo/MS_1001456 analysis software http://purl.obolibrary.org/obo/MS_1000531 software Analysis software. http://purl.obolibrary.org/obo/MS_1001457 data processing software http://purl.obolibrary.org/obo/MS_1000531 software Data processing software. http://purl.obolibrary.org/obo/MS_1001460 unknown modification http://purl.obolibrary.org/obo/MS_1001471 peptide modification details This term should be given if the modification was unknown. http://purl.obolibrary.org/obo/MS_1001461 greylag http://purl.obolibrary.org/obo/MS_1001456 analysis software Greylag identification software. http://purl.obolibrary.org/obo/MS_1001462 PEFF format http://purl.obolibrary.org/obo/MS_1001347 database file formats The sequence database was stored in the PEFF (PSI enhanced FastA file) format. http://purl.obolibrary.org/obo/MS_1001463 Phenyx XML format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Phenyx open XML file format. http://purl.obolibrary.org/obo/MS_1001464 DTASelect format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format DTASelect file format. http://purl.obolibrary.org/obo/MS_1001466 MS2 format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format MS2 file format for MS2 spectral data. http://purl.obolibrary.org/obo/MS_1001467 taxonomy: NCBI TaxID http://purl.obolibrary.org/obo/MS_1001089 molecule taxonomy This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens. http://purl.obolibrary.org/obo/MS_1001468 taxonomy: common name http://purl.obolibrary.org/obo/MS_1001089 molecule taxonomy This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. http://purl.obolibrary.org/obo/MS_1001469 taxonomy: scientific name http://purl.obolibrary.org/obo/MS_1001089 molecule taxonomy This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. http://purl.obolibrary.org/obo/MS_1001470 taxonomy: Swiss-Prot ID http://purl.obolibrary.org/obo/MS_1001089 molecule taxonomy This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. http://purl.obolibrary.org/obo/MS_1001472 selected ion monitoring chromatogram http://purl.obolibrary.org/obo/MS_1000810 ion current chromatogram Representation of an array of the measurements of a selectively monitored ion versus time. http://purl.obolibrary.org/obo/MS_1001473 selected reaction monitoring chromatogram http://purl.obolibrary.org/obo/MS_1000810 ion current chromatogram Representation of an array of the measurements of a selectively monitored reaction versus time. http://purl.obolibrary.org/obo/MS_1001474 consecutive reaction monitoring chromatogram http://purl.obolibrary.org/obo/MS_1000810 ion current chromatogram OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time. http://purl.obolibrary.org/obo/MS_1001475 OMSSA http://purl.obolibrary.org/obo/MS_1001456 analysis software Open Mass Spectrometry Search Algorithm was used to analyze the spectra. http://purl.obolibrary.org/obo/MS_1001476 X!Tandem http://purl.obolibrary.org/obo/MS_1001456 analysis software X!Tandem was used to analyze the spectra. http://purl.obolibrary.org/obo/MS_1001477 SpectraST http://purl.obolibrary.org/obo/MS_1003207 library creation software Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline. http://purl.obolibrary.org/obo/MS_1001478 Mascot Parser http://purl.obolibrary.org/obo/MS_1001456 analysis software Mascot Parser was used to analyze the spectra. http://purl.obolibrary.org/obo/MS_1001479 null-terminated ASCII string http://purl.obolibrary.org/obo/MS_1000518 binary data type Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte. http://purl.obolibrary.org/obo/MS_1001480 SCIEX TOF/TOF nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1001481 SCIEX TOF/TOF database http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database. http://purl.obolibrary.org/obo/MS_1001482 5800 TOF/TOF http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument SCIEX 5800 TOF-TOF Analyzer. http://purl.obolibrary.org/obo/MS_1001483 SCIEX TOF/TOF Series Explorer Software http://purl.obolibrary.org/obo/MS_1001457 data processing software SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1001484 intensity normalization http://purl.obolibrary.org/obo/MS_1000543 data processing action Normalization of data point intensities. http://purl.obolibrary.org/obo/MS_1001485 m/z calibration http://purl.obolibrary.org/obo/MS_1000543 data processing action Calibration of data point m/z positions. http://purl.obolibrary.org/obo/MS_1001486 data filtering http://purl.obolibrary.org/obo/MS_1000543 data processing action Filtering out part of the data. http://purl.obolibrary.org/obo/MS_1001487 ProteinExtractor http://purl.obolibrary.org/obo/MS_1001456 analysis software An algorithm for protein determination/assembly integrated into Bruker's ProteinScape. http://purl.obolibrary.org/obo/MS_1001488 Mascot Distiller http://purl.obolibrary.org/obo/MS_1001456 analysis software Mascot Distiller. http://purl.obolibrary.org/obo/MS_1001489 Mascot Integra http://purl.obolibrary.org/obo/MS_1001456 analysis software Mascot Integra. http://purl.obolibrary.org/obo/MS_1001490 Percolator http://purl.obolibrary.org/obo/MS_1001456 analysis software Percolator. http://purl.obolibrary.org/obo/MS_1001491 percolator:Q value http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Percolator:Q value. http://purl.obolibrary.org/obo/MS_1001492 percolator:score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Percolator:score. http://purl.obolibrary.org/obo/MS_1001493 percolator:PEP http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Posterior error probability. http://purl.obolibrary.org/obo/MS_1001494 no threshold http://purl.obolibrary.org/obo/MS_1002482 statistical threshold In case no threshold was used. http://purl.obolibrary.org/obo/MS_1001495 ProteinScape:SearchResultId http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SearchResultId of this peptide as SearchResult in the ProteinScape database. http://purl.obolibrary.org/obo/MS_1001496 ProteinScape:SearchEventId http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SearchEventId of the SearchEvent in the ProteinScape database. http://purl.obolibrary.org/obo/MS_1001497 ProteinScape:ProfoundProbability http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Profound probability score stored by ProteinScape. http://purl.obolibrary.org/obo/MS_1001498 Profound:z value http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Profound z value. http://purl.obolibrary.org/obo/MS_1001499 Profound:Cluster http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Profound cluster score. http://purl.obolibrary.org/obo/MS_1001500 Profound:ClusterRank http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Profound cluster rank. http://purl.obolibrary.org/obo/MS_1001501 MSFit:Mowse score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The MSFit Mowse score. http://purl.obolibrary.org/obo/MS_1001502 Sonar:Score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Sonar score. http://purl.obolibrary.org/obo/MS_1001503 ProteinScape:PFFSolverExp http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The ProteinSolver exp value stored by ProteinScape. http://purl.obolibrary.org/obo/MS_1001504 ProteinScape:PFFSolverScore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The ProteinSolver score stored by ProteinScape. http://purl.obolibrary.org/obo/MS_1001505 ProteinScape:IntensityCoverage http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape. http://purl.obolibrary.org/obo/MS_1001506 ProteinScape:SequestMetaScore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores. http://purl.obolibrary.org/obo/MS_1001507 ProteinExtractor:Score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The score calculated by ProteinExtractor. http://purl.obolibrary.org/obo/MS_1001508 Agilent MassHunter nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by scanId=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1001509 Agilent MassHunter format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer. http://purl.obolibrary.org/obo/MS_1001510 TSQ Vantage http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument TSQ Vantage. http://purl.obolibrary.org/obo/MS_1001511 Sequence database filter types http://purl.obolibrary.org/obo/MS_1001019 database filtering Filter types which are used to filter a sequence database. http://purl.obolibrary.org/obo/MS_1001512 Sequence database filters http://purl.obolibrary.org/obo/MS_1001019 database filtering Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search. http://purl.obolibrary.org/obo/MS_1001513 DB sequence filter pattern http://purl.obolibrary.org/obo/MS_1001512 Sequence database filters DB sequence filter pattern. http://purl.obolibrary.org/obo/MS_1001514 DB accession filter string http://purl.obolibrary.org/obo/MS_1001512 Sequence database filters DB accession filter string. http://purl.obolibrary.org/obo/MS_1001515 frag: c ion - H2O http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: c ion without water. http://purl.obolibrary.org/obo/MS_1001516 frag: c ion - NH3 http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: c ion without ammonia. http://purl.obolibrary.org/obo/MS_1001517 frag: z ion - H2O http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: z ion without water. http://purl.obolibrary.org/obo/MS_1001518 frag: z ion - NH3 http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: z ion without ammonia. http://purl.obolibrary.org/obo/MS_1001519 frag: x ion - H2O http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: x ion without water. http://purl.obolibrary.org/obo/MS_1001520 frag: x ion - NH3 http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: x ion without ammonia. http://purl.obolibrary.org/obo/MS_1001521 frag: precursor ion - H2O http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: precursor ion without water. http://purl.obolibrary.org/obo/MS_1001522 frag: precursor ion - NH3 http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: precursor ion without ammonia. http://purl.obolibrary.org/obo/MS_1001523 frag: precursor ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragmentation information, type of product: precursor ion. http://purl.obolibrary.org/obo/MS_1001524 fragment neutral loss http://purl.obolibrary.org/obo/MS_1001471 peptide modification details This term can describe a neutral loss m/z value that is lost from an ion. http://purl.obolibrary.org/obo/MS_1001525 precursor neutral loss http://purl.obolibrary.org/obo/MS_1001471 peptide modification details This term can describe a neutral loss m/z value that is lost from an ion. http://purl.obolibrary.org/obo/MS_1001526 spectrum from database integer nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by databasekey=xsd:long. http://purl.obolibrary.org/obo/MS_1001527 Proteinscape spectra http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Spectra from Bruker/Protagen Proteinscape database. http://purl.obolibrary.org/obo/MS_1001528 Mascot query number http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Native format defined by query=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1001529 spectra data details http://purl.obolibrary.org/obo/MS_1001249 search input details Child-terms contain information to map the results back to spectra. http://purl.obolibrary.org/obo/MS_1001530 mzML unique identifier http://purl.obolibrary.org/obo/MS_1001529 spectra data details Native format defined by mzMLid=xsd:IDREF. http://purl.obolibrary.org/obo/MS_1001531 spectrum from ProteinScape database nativeID format http://purl.obolibrary.org/obo/MS_1001529 spectra data details Native format defined by databasekey=xsd:long. http://purl.obolibrary.org/obo/MS_1001532 spectrum from database string nativeID format http://purl.obolibrary.org/obo/MS_1001529 spectra data details Native format defined by databasekey=xsd:string. http://purl.obolibrary.org/obo/MS_1001533 Bruker Daltonics esquire series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' esquire series. http://purl.obolibrary.org/obo/MS_1001534 Bruker Daltonics flex series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' flex series. http://purl.obolibrary.org/obo/MS_1001535 Bruker Daltonics BioTOF series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' BioTOF series. http://purl.obolibrary.org/obo/MS_1001536 Bruker Daltonics micrOTOF series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' micrOTOF series. http://purl.obolibrary.org/obo/MS_1001537 BioTOF http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' BioTOF: ESI TOF. http://purl.obolibrary.org/obo/MS_1001538 BioTOF III http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' BioTOF III: ESI TOF. http://purl.obolibrary.org/obo/MS_1001539 UltroTOF-Q http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional). http://purl.obolibrary.org/obo/MS_1001540 micrOTOF II http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1001541 maXis http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI. http://purl.obolibrary.org/obo/MS_1001542 amaZon ETD http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR. http://purl.obolibrary.org/obo/MS_1001543 microflex LRF http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' microflex LRF: MALDI TOF. http://purl.obolibrary.org/obo/MS_1001544 ultrafleXtreme http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker Daltonics' ultrafleXtreme: MALDI TOF. http://purl.obolibrary.org/obo/MS_1001545 Bruker Daltonics amaZon series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' amaZon series. http://purl.obolibrary.org/obo/MS_1001546 amaZon X http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. http://purl.obolibrary.org/obo/MS_1001547 Bruker Daltonics maXis series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' maXis series. http://purl.obolibrary.org/obo/MS_1001548 Bruker Daltonics solarix series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. http://purl.obolibrary.org/obo/MS_1001549 solariX http://purl.obolibrary.org/obo/MS_1003766 quadrupole fourier transform ion cyclotron resonance instrument Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR. http://purl.obolibrary.org/obo/MS_1001550 microflex II http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' microflex II: MALDI TOF. http://purl.obolibrary.org/obo/MS_1001553 autoflex II TOF/TOF http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF. http://purl.obolibrary.org/obo/MS_1001554 autoflex III TOF/TOF smartbeam http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF. http://purl.obolibrary.org/obo/MS_1001555 autoflex http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker Daltonics' autoflex: MALDI TOF. http://purl.obolibrary.org/obo/MS_1001556 Bruker Daltonics apex series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' apex series. http://purl.obolibrary.org/obo/MS_1001557 Shimadzu Corporation software http://purl.obolibrary.org/obo/MS_1000531 software Shimadzu Corporation software. http://purl.obolibrary.org/obo/MS_1001558 MALDI Solutions http://purl.obolibrary.org/obo/MS_1001557 Shimadzu Corporation software Shimadzu Biotech software for data acquisition, processing, and analysis. http://purl.obolibrary.org/obo/MS_1001559 SCIEX TOF/TOF T2D nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by file=xsd:IDREF. http://purl.obolibrary.org/obo/MS_1001560 SCIEX TOF/TOF T2D format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format. http://purl.obolibrary.org/obo/MS_1001561 Scaffold http://purl.obolibrary.org/obo/MS_1001456 analysis software Scaffold analysis software. http://purl.obolibrary.org/obo/MS_1001562 Scaffold nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Scaffold native ID format. http://purl.obolibrary.org/obo/MS_1001563 SEQUEST SQT format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in SEQUEST SQT format. http://purl.obolibrary.org/obo/MS_1001564 Discoverer MSF format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format. http://purl.obolibrary.org/obo/MS_1001565 IdentityE XML format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in Waters IdentityE XML format. http://purl.obolibrary.org/obo/MS_1001566 ProteinLynx XML format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in Waters ProteinLynx XML format. http://purl.obolibrary.org/obo/MS_1001567 SpectrumMill directories http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Source file for this mzIdentML was in Agilent SpectrumMill directory format. http://purl.obolibrary.org/obo/MS_1001568 Scaffold:Peptide Probability http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Scaffold peptide probability score. http://purl.obolibrary.org/obo/MS_1001569 IdentityE Score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Waters IdentityE peptide score. http://purl.obolibrary.org/obo/MS_1001570 ProteinLynx:Log Likelihood http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic ProteinLynx log likelihood score. http://purl.obolibrary.org/obo/MS_1001571 ProteinLynx:Ladder Score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Waters ProteinLynx Ladder score. http://purl.obolibrary.org/obo/MS_1001572 SpectrumMill:Score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Spectrum mill peptide score. http://purl.obolibrary.org/obo/MS_1001573 SpectrumMill:SPI http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic SpectrumMill SPI score (%). http://purl.obolibrary.org/obo/MS_1001574 report only spectra assigned to identified proteins http://purl.obolibrary.org/obo/MS_1001060 quality estimation method details Flag indicating to report only the spectra assigned to identified proteins. http://purl.obolibrary.org/obo/MS_1001575 Scaffold: Minimum Peptide Count http://purl.obolibrary.org/obo/MS_1002106 Scaffold input parameter Minimum number of peptides a protein must have to be accepted. http://purl.obolibrary.org/obo/MS_1001576 Scaffold: Minimum Protein Probability http://purl.obolibrary.org/obo/MS_1002106 Scaffold input parameter Minimum protein probability a protein must have to be accepted. http://purl.obolibrary.org/obo/MS_1001577 Scaffold: Minimum Peptide Probability http://purl.obolibrary.org/obo/MS_1002106 Scaffold input parameter Minimum probability a peptide must have to be accepted for protein scoring. http://purl.obolibrary.org/obo/MS_1001578 minimum number of enzymatic termini http://purl.obolibrary.org/obo/MS_1002094 common search engine input parameter Minimum number of enzymatic termini a peptide must have to be accepted. http://purl.obolibrary.org/obo/MS_1001579 Scaffold:Protein Probability http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins Scaffold protein probability score. http://purl.obolibrary.org/obo/MS_1001580 SpectrumMill:Discriminant Score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Discriminant score from Agilent SpectrumMill software. http://purl.obolibrary.org/obo/MS_1001581 FAIMS compensation voltage http://purl.obolibrary.org/obo/MS_1003254 peak attribute The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion. http://purl.obolibrary.org/obo/MS_1001582 XCMS http://purl.obolibrary.org/obo/MS_1001457 data processing software Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data. http://purl.obolibrary.org/obo/MS_1001583 MaxQuant http://purl.obolibrary.org/obo/MS_1001456 analysis software MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data. http://purl.obolibrary.org/obo/MS_1001584 combined pmf + ms-ms search http://purl.obolibrary.org/obo/MS_1001080 search type Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF). http://purl.obolibrary.org/obo/MS_1001585 MyriMatch http://purl.obolibrary.org/obo/MS_1001456 analysis software Tabb Lab software for directly comparing peptides in a database to tandem mass spectra. http://purl.obolibrary.org/obo/MS_1001586 DirecTag http://purl.obolibrary.org/obo/MS_1001456 analysis software Tabb Lab software for generating sequence tags from tandem mass spectra. http://purl.obolibrary.org/obo/MS_1001587 TagRecon http://purl.obolibrary.org/obo/MS_1001456 analysis software Tabb Lab software for reconciling sequence tags to a protein database. http://purl.obolibrary.org/obo/MS_1001588 Pepitome http://purl.obolibrary.org/obo/MS_1001456 analysis software Tabb Lab software for spectral library searches on tandem mass spectra. http://purl.obolibrary.org/obo/MS_1001589 MyriMatch:MVH http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance. http://purl.obolibrary.org/obo/MS_1001590 MyriMatch:mzFidelity http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution. http://purl.obolibrary.org/obo/MS_1001591 anchor protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A representative protein selected from a set of sequence same-set or spectrum same-set proteins. http://purl.obolibrary.org/obo/MS_1001592 family member protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A protein with significant homology to another protein, but some distinguishing peptide matches. http://purl.obolibrary.org/obo/MS_1001593 group member with undefined relationship OR ortholog protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship TO ENDETAIL: a really generic relationship OR ortholog protein. http://purl.obolibrary.org/obo/MS_1001594 sequence same-set protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences. http://purl.obolibrary.org/obo/MS_1001595 spectrum same-set protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra. http://purl.obolibrary.org/obo/MS_1001596 sequence sub-set protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches. http://purl.obolibrary.org/obo/MS_1001597 spectrum sub-set protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches. http://purl.obolibrary.org/obo/MS_1001598 sequence subsumable protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins. http://purl.obolibrary.org/obo/MS_1001599 spectrum subsumable protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins. http://purl.obolibrary.org/obo/MS_1001600 protein inference confidence category http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable). http://purl.obolibrary.org/obo/MS_1001601 ProteomeDiscoverer:Spectrum Files:Raw File names http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Name and location of the .raw file or files. http://purl.obolibrary.org/obo/MS_1001602 ProteomeDiscoverer:SRF File Selector:SRF File Path http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Path and name of the .srf (SEQUEST Result Format) file. http://purl.obolibrary.org/obo/MS_1001603 ProteomeDiscoverer:Spectrum Selector:Ionization Source http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc). http://purl.obolibrary.org/obo/MS_1001604 ProteomeDiscoverer:Activation Type http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any). http://purl.obolibrary.org/obo/MS_1001605 ProteomeDiscoverer:Spectrum Selector:Lower RT Limit http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Lower retention-time limit. http://purl.obolibrary.org/obo/MS_1001606 ProteomeDiscoverer:Mass Analyzer http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS). http://purl.obolibrary.org/obo/MS_1001607 ProteomeDiscoverer:Max Precursor Mass http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum mass limit of a singly charged precursor ion. http://purl.obolibrary.org/obo/MS_1001608 ProteomeDiscoverer:Min Precursor Mass http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimum mass limit of a singly charged precursor ion. http://purl.obolibrary.org/obo/MS_1001609 ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow. http://purl.obolibrary.org/obo/MS_1001610 ProteomeDiscoverer:MS Order http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Level of the mass spectrum (MS2 ... MS10). http://purl.obolibrary.org/obo/MS_1001611 ProteomeDiscoverer:Polarity Mode http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Polarity mode (positive or negative). http://purl.obolibrary.org/obo/MS_1001612 ProteomeDiscoverer:Spectrum Selector:Precursor Selection http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3). http://purl.obolibrary.org/obo/MS_1001613 ProteomeDiscoverer:SN Threshold http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Signal-to-Noise ratio below which peaks are removed. http://purl.obolibrary.org/obo/MS_1001614 ProteomeDiscoverer:Scan Type http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM)). http://purl.obolibrary.org/obo/MS_1001615 ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value. http://purl.obolibrary.org/obo/MS_1001616 ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header. http://purl.obolibrary.org/obo/MS_1001617 ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the charge state of the precursor ions, if it is not defined in the scan header. http://purl.obolibrary.org/obo/MS_1001618 ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header. http://purl.obolibrary.org/obo/MS_1001619 ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header. http://purl.obolibrary.org/obo/MS_1001620 ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the polarity of the ions monitored if it is not included in the scan header. http://purl.obolibrary.org/obo/MS_1001621 ProteomeDiscoverer:Spectrum Selector:Upper RT Limit http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Upper retention-time limit. http://purl.obolibrary.org/obo/MS_1001622 ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors. http://purl.obolibrary.org/obo/MS_1001623 ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum allowed mass of a neutral loss. http://purl.obolibrary.org/obo/MS_1001624 ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed. http://purl.obolibrary.org/obo/MS_1001625 ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether neutral loss peaks are removed from ETD and ECD spectra. http://purl.obolibrary.org/obo/MS_1001626 ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra. http://purl.obolibrary.org/obo/MS_1001627 ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum. http://purl.obolibrary.org/obo/MS_1001628 ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether precursor artifact peaks from the MS2 input spectra are removed. http://purl.obolibrary.org/obo/MS_1001629 ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type. http://purl.obolibrary.org/obo/MS_1001630 ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether spectra from different MS order scans can be grouped together. http://purl.obolibrary.org/obo/MS_1001631 ProteomeDiscoverer:Spectrum Grouper:Max RT Difference http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species. http://purl.obolibrary.org/obo/MS_1001632 ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis. http://purl.obolibrary.org/obo/MS_1001633 ProteomeDiscoverer:Xtract:Highest Charge http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Highest charge state that is allowed for the deconvolution of multiply charged data. http://purl.obolibrary.org/obo/MS_1001634 ProteomeDiscoverer:Xtract:Highest MZ http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. http://purl.obolibrary.org/obo/MS_1001635 ProteomeDiscoverer:Xtract:Lowest Charge http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Lowest charge state that is allowed for the deconvolution of multiply charged data. http://purl.obolibrary.org/obo/MS_1001636 ProteomeDiscoverer:Xtract:Lowest MZ http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. http://purl.obolibrary.org/obo/MS_1001637 ProteomeDiscoverer:Xtract:Monoisotopic Mass Only http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum. http://purl.obolibrary.org/obo/MS_1001638 ProteomeDiscoverer:Xtract:Overlapping Remainder http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted). http://purl.obolibrary.org/obo/MS_1001639 ProteomeDiscoverer:Xtract:Required Fitting Accuracy http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Accuracy required for a pattern fit to be considered valid. http://purl.obolibrary.org/obo/MS_1001640 ProteomeDiscoverer:Xtract:Resolution At 400 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Resolution at mass 400. http://purl.obolibrary.org/obo/MS_1001641 ProteomeDiscoverer:Lowest Charge State http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimum charge state below which peptides are filtered out. http://purl.obolibrary.org/obo/MS_1001642 ProteomeDiscoverer:Highest Charge State http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum charge above which peptides are filtered out. http://purl.obolibrary.org/obo/MS_1001643 ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether spectra with scores above the threshold score are retained rather than filtered out. http://purl.obolibrary.org/obo/MS_1001644 ProteomeDiscoverer:Dynamic Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determine dynamic post-translational modifications (PTMs). http://purl.obolibrary.org/obo/MS_1001645 ProteomeDiscoverer:Static Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Static Modification to all occurrences of a named amino acid. http://purl.obolibrary.org/obo/MS_1001646 ProteomeDiscoverer:Mascot:Decoy Search http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database. http://purl.obolibrary.org/obo/MS_1001647 ProteomeDiscoverer:Mascot:Error tolerant Search http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether to search error-tolerant. http://purl.obolibrary.org/obo/MS_1001648 ProteomeDiscoverer:Mascot:Max MGF File Size http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum size of the .mgf (Mascot Generic Format) file in MByte. http://purl.obolibrary.org/obo/MS_1001649 ProteomeDiscoverer:Mascot:Mascot Server URL http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter URL (Uniform resource Locator) of the Mascot server. http://purl.obolibrary.org/obo/MS_1001650 ProteomeDiscoverer:Mascot:Number of attempts to submit the search http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Number of attempts to submit the Mascot search. http://purl.obolibrary.org/obo/MS_1001651 ProteomeDiscoverer:Mascot:X Static Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Number of attempts to submit the Mascot search. http://purl.obolibrary.org/obo/MS_1001652 ProteomeDiscoverer:Mascot:User Name http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Name of the user submitting the Mascot search. http://purl.obolibrary.org/obo/MS_1001653 ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Time interval between attempts to submit a search in seconds. http://purl.obolibrary.org/obo/MS_1001654 ProteomeDiscoverer:Enzyme Name http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Specifies the enzyme reagent used for protein digestion. http://purl.obolibrary.org/obo/MS_1001655 ProteomeDiscoverer:Fragment Mass Tolerance http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu. http://purl.obolibrary.org/obo/MS_1001656 Mascot:Instrument http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter Type of instrument used to acquire the data in the raw file. http://purl.obolibrary.org/obo/MS_1001657 ProteomeDiscoverer:Maximum Missed Cleavage Sites http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum number of missed cleavage sites to consider during the digest. http://purl.obolibrary.org/obo/MS_1001658 ProteomeDiscoverer:Mascot:Peptide CutOff Score http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimum score in the IonScore column that each peptide must exceed in order to be reported. http://purl.obolibrary.org/obo/MS_1001659 ProteomeDiscoverer:Precursor Mass Tolerance http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Mass window for which precursor ions are considered to be the same species. http://purl.obolibrary.org/obo/MS_1001660 ProteomeDiscoverer:Mascot:Protein CutOff Score http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimum protein score in the IonScore column that each protein must exceed in order to be reported. http://purl.obolibrary.org/obo/MS_1001661 ProteomeDiscoverer:Protein Database http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Database to use in the search (configured on the Mascot server). http://purl.obolibrary.org/obo/MS_1001662 ProteomeDiscoverer:Mascot:Protein Relevance Factor http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report. http://purl.obolibrary.org/obo/MS_1001663 ProteomeDiscoverer:Target FDR Relaxed http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence. http://purl.obolibrary.org/obo/MS_1001664 ProteomeDiscoverer:Target FDR Strict http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence. http://purl.obolibrary.org/obo/MS_1001665 ProteomeDiscoverer:Mascot:Taxonomy http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Limits searches to entries from a particular species or group of species. http://purl.obolibrary.org/obo/MS_1001666 ProteomeDiscoverer:Use Average Precursor Mass http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Use average mass for the precursor. http://purl.obolibrary.org/obo/MS_1001667 Mascot:use MudPIT scoring http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter OBSOLETE Determines whether to use MudPIT or normal scoring. http://purl.obolibrary.org/obo/MS_1001668 ProteomeDiscoverer:Absolute XCorr Threshold http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported. http://purl.obolibrary.org/obo/MS_1001669 ProteomeDiscoverer:SEQUEST:Calculate Probability Score http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether to calculate a probability score for every peptide match. http://purl.obolibrary.org/obo/MS_1001670 ProteomeDiscoverer:SEQUEST:CTerminal Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Dynamic C-terminal modification that is used during the search. http://purl.obolibrary.org/obo/MS_1001671 ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained. http://purl.obolibrary.org/obo/MS_1001672 ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum number of identical modifications that a single peptide can have. http://purl.obolibrary.org/obo/MS_1001673 ProteomeDiscoverer:Max Modifications Per Peptide http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance. http://purl.obolibrary.org/obo/MS_1001674 ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum number of peptides that are searched and scored per spectrum. http://purl.obolibrary.org/obo/MS_1001675 ProteomeDiscoverer:Maximum Peptides Output http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum number of peptide matches reported per spectrum. http://purl.obolibrary.org/obo/MS_1001676 ProteomeDiscoverer:Maximum Protein References Per Peptide http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum number of proteins that a single identified peptide can be associated with during protein assembly. http://purl.obolibrary.org/obo/MS_1001677 ProteomeDiscoverer:SEQUEST:NTerminal Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Dynamic N-terminal modification that is used during the search. http://purl.obolibrary.org/obo/MS_1001678 ProteomeDiscoverer:Peptide CTerminus http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Static modification for the C terminal of the peptide used during the search. http://purl.obolibrary.org/obo/MS_1001679 ProteomeDiscoverer:Peptide NTerminus http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Static modification for the N terminal of the peptide used during the search. http://purl.obolibrary.org/obo/MS_1001680 ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies a factor to apply to the protein score. http://purl.obolibrary.org/obo/MS_1001681 ProteomeDiscoverer:Protein Relevance Threshold http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report. http://purl.obolibrary.org/obo/MS_1001682 ProteomeDiscoverer:Search Against Decoy Database http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database. http://purl.obolibrary.org/obo/MS_1001683 ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Use average masses for the fragments. http://purl.obolibrary.org/obo/MS_1001684 ProteomeDiscoverer:Use Neutral Loss a Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether a ions with neutral loss are used for spectrum matching. http://purl.obolibrary.org/obo/MS_1001685 ProteomeDiscoverer:Use Neutral Loss b Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether b ions with neutral loss are used for spectrum matching. http://purl.obolibrary.org/obo/MS_1001686 ProteomeDiscoverer:Use Neutral Loss y Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether y ions with neutral loss are used for spectrum matching. http://purl.obolibrary.org/obo/MS_1001687 ProteomeDiscoverer:Use Neutral Loss z Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines whether z ions with neutral loss are used for spectrum matching. http://purl.obolibrary.org/obo/MS_1001688 ProteomeDiscoverer:SEQUEST:Weight of a Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Uses a ions for spectrum matching with this relative factor. http://purl.obolibrary.org/obo/MS_1001689 ProteomeDiscoverer:SEQUEST:Weight of b Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Uses b ions for spectrum matching with this relative factor. http://purl.obolibrary.org/obo/MS_1001690 ProteomeDiscoverer:SEQUEST:Weight of c Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Uses c ions for spectrum matching with this relative factor. http://purl.obolibrary.org/obo/MS_1001691 ProteomeDiscoverer:SEQUEST:Weight of d Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Uses c ions for spectrum matching with this relative factor. http://purl.obolibrary.org/obo/MS_1001692 ProteomeDiscoverer:SEQUEST:Weight of v Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Uses c ions for spectrum matching with this relative factor. http://purl.obolibrary.org/obo/MS_1001693 ProteomeDiscoverer:SEQUEST:Weight of w Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Uses c ions for spectrum matching with this relative factor. http://purl.obolibrary.org/obo/MS_1001694 ProteomeDiscoverer:SEQUEST:Weight of x Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Uses x ions for spectrum matching with this relative factor. http://purl.obolibrary.org/obo/MS_1001695 ProteomeDiscoverer:SEQUEST:Weight of y Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Uses y ions for spectrum matching with this relative factor. http://purl.obolibrary.org/obo/MS_1001696 ProteomeDiscoverer:SEQUEST:Weight of z Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Uses z ions for spectrum matching with this relative factor. http://purl.obolibrary.org/obo/MS_1001697 ProteomeDiscoverer:ZCore:Protein Score Cutoff http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Sets a minimum protein score that each protein must exceed in order to be reported. http://purl.obolibrary.org/obo/MS_1001698 ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies which peak to select if more than one peak is found inside the integration window. http://purl.obolibrary.org/obo/MS_1001699 ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the mass-to-charge window that enables one to look for the reporter peaks. http://purl.obolibrary.org/obo/MS_1001700 ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Quantitation method for isobarically labeled quantitation. http://purl.obolibrary.org/obo/MS_1001701 ProteomeDiscoverer:Spectrum Exporter:Export Format http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Format of the exported spectra (dta, mgf or mzData). http://purl.obolibrary.org/obo/MS_1001702 ProteomeDiscoverer:Spectrum Exporter:File name http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Name of the output file that contains the exported data. http://purl.obolibrary.org/obo/MS_1001703 ProteomeDiscoverer:Search Modifications Only For Identified Proteins http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Influences the modifications search. http://purl.obolibrary.org/obo/MS_1001704 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Standard high confidence XCorr parameter for charge = 1. http://purl.obolibrary.org/obo/MS_1001705 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Standard high confidence XCorr parameter for charge = 2. http://purl.obolibrary.org/obo/MS_1001706 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Standard high confidence XCorr parameter for charge = 3. http://purl.obolibrary.org/obo/MS_1001707 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Standard high confidence XCorr parameter for charge >= 4. http://purl.obolibrary.org/obo/MS_1001708 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Standard medium confidence XCorr parameter for charge = 1. http://purl.obolibrary.org/obo/MS_1001709 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Standard medium confidence XCorr parameter for charge = 2. http://purl.obolibrary.org/obo/MS_1001710 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Standard medium confidence XCorr parameter for charge = 3. http://purl.obolibrary.org/obo/MS_1001711 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Standard medium confidence XCorr parameter for charge >= 4. http://purl.obolibrary.org/obo/MS_1001712 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter FT high confidence XCorr parameter for charge = 1. http://purl.obolibrary.org/obo/MS_1001713 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter FT high confidence XCorr parameter for charge = 2. http://purl.obolibrary.org/obo/MS_1001714 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter FT high confidence XCorr parameter for charge = 3. http://purl.obolibrary.org/obo/MS_1001715 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter FT high confidence XCorr parameter for charge >= 4. http://purl.obolibrary.org/obo/MS_1001716 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter FT medium confidence XCorr parameter for charge = 1. http://purl.obolibrary.org/obo/MS_1001717 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter FT medium confidence XCorr parameter for charge = 2. http://purl.obolibrary.org/obo/MS_1001718 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter FT medium confidence XCorr parameter for charge = 3. http://purl.obolibrary.org/obo/MS_1001719 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4 http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter FT medium confidence XCorr parameter for charge >= 4. http://purl.obolibrary.org/obo/MS_1001720 ProteomeDiscoverer:1. Dynamic Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter. http://purl.obolibrary.org/obo/MS_1001721 ProteomeDiscoverer:2. Dynamic Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter. http://purl.obolibrary.org/obo/MS_1001722 ProteomeDiscoverer:3. Dynamic Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter. http://purl.obolibrary.org/obo/MS_1001723 ProteomeDiscoverer:4. Dynamic Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter. http://purl.obolibrary.org/obo/MS_1001724 ProteomeDiscoverer:Static Modification for X http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Static Modification for X. http://purl.obolibrary.org/obo/MS_1001725 ProteomeDiscoverer:Initial minimal peptide probability http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimal initial peptide probability to contribute to analysis. http://purl.obolibrary.org/obo/MS_1001726 ProteomeDiscoverer:Minimal peptide probability http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimum adjusted peptide probability contributing to protein probability. http://purl.obolibrary.org/obo/MS_1001727 ProteomeDiscoverer:Minimal peptide weight http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimum peptide weight contributing to protein probability. http://purl.obolibrary.org/obo/MS_1001728 ProteomeDiscoverer:Number of input1 spectra http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Number of spectra from 1+ precursor ions. http://purl.obolibrary.org/obo/MS_1001729 ProteomeDiscoverer:Number of input2 spectra http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Number of spectra from 2+ precursor ions. http://purl.obolibrary.org/obo/MS_1001730 ProteomeDiscoverer:Number of input3 spectra http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Number of spectra from 3+ precursor ions. http://purl.obolibrary.org/obo/MS_1001731 ProteomeDiscoverer:Number of input4 spectra http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Number of spectra from 4+ precursor ions. http://purl.obolibrary.org/obo/MS_1001732 ProteomeDiscoverer:Number of input5 spectra http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Number of spectra from 5+ precursor ions. http://purl.obolibrary.org/obo/MS_1001733 ProteomeDiscoverer:Number of predicted correct proteins http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Total number of predicted correct protein ids (sum of probabilities). http://purl.obolibrary.org/obo/MS_1001734 ProteomeDiscoverer:Organism http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Sample organism (used for annotation purposes). http://purl.obolibrary.org/obo/MS_1001735 ProteomeDiscoverer:Reference Database http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Full path database name. http://purl.obolibrary.org/obo/MS_1001736 ProteomeDiscoverer:Residue substitution list http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Residues considered equivalent when comparing peptides. http://purl.obolibrary.org/obo/MS_1001737 ProteomeDiscoverer:Source file extension http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE File type (if not pepXML). http://purl.obolibrary.org/obo/MS_1001738 ProteomeDiscoverer:Source Files http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Input pepXML files. http://purl.obolibrary.org/obo/MS_1001739 ProteomeDiscoverer:Source Files old http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE Input pepXML files (old). http://purl.obolibrary.org/obo/MS_1001740 ProteomeDiscoverer:WinCyg reference database http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Windows full path for database. http://purl.obolibrary.org/obo/MS_1001741 ProteomeDiscoverer:WinCyg source files http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Windows pepXML file names. http://purl.obolibrary.org/obo/MS_1001742 LTQ Orbitrap Velos http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Finnigan LTQ Orbitrap Velos MS. http://purl.obolibrary.org/obo/MS_1001743 ProteomeDiscoverer:Mascot:Weight of A Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use A ions for spectrum matching. http://purl.obolibrary.org/obo/MS_1001744 ProteomeDiscoverer:Mascot:Weight of B Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use B ions for spectrum matching. http://purl.obolibrary.org/obo/MS_1001745 ProteomeDiscoverer:Mascot:Weight of C Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use C ions for spectrum matching. http://purl.obolibrary.org/obo/MS_1001746 ProteomeDiscoverer:Mascot:Weight of D Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use D ions for spectrum matching. http://purl.obolibrary.org/obo/MS_1001747 ProteomeDiscoverer:Mascot:Weight of V Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use V ions for spectrum matching. http://purl.obolibrary.org/obo/MS_1001748 ProteomeDiscoverer:Mascot:Weight of W Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use W ions for spectrum matching. http://purl.obolibrary.org/obo/MS_1001749 ProteomeDiscoverer:Mascot:Weight of X Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use X ions for spectrum matching. http://purl.obolibrary.org/obo/MS_1001750 ProteomeDiscoverer:Mascot:Weight of Y Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use Y ions for spectrum matching. http://purl.obolibrary.org/obo/MS_1001751 ProteomeDiscoverer:Mascot:Weight of Z Ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use z ions for spectrum matching. http://purl.obolibrary.org/obo/MS_1001752 ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determines if to use precursor reevaluation. http://purl.obolibrary.org/obo/MS_1001753 ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Signal-to-Noise ratio below which peaks are removed (in FT mode only). http://purl.obolibrary.org/obo/MS_1001754 ProteomeDiscoverer:Mascot:Please Do not Touch this http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches. http://purl.obolibrary.org/obo/MS_1001755 contact phone number http://purl.obolibrary.org/obo/MS_1000585 contact attribute Phone number of the contact person or organization. http://purl.obolibrary.org/obo/MS_1001756 contact fax number http://purl.obolibrary.org/obo/MS_1000585 contact attribute Fax number for the contact person or organization. http://purl.obolibrary.org/obo/MS_1001757 contact toll-free phone number http://purl.obolibrary.org/obo/MS_1000585 contact attribute Toll-free phone number of the contact person or organization. http://purl.obolibrary.org/obo/MS_1001758 Mascot:SigThresholdType http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter Significance threshold type used in Mascot reporting (either 'identity' or 'homology'). http://purl.obolibrary.org/obo/MS_1001759 Mascot:ProteinGrouping http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering'). http://purl.obolibrary.org/obo/MS_1001760 Percolator:features http://purl.obolibrary.org/obo/MS_1002107 Percolator input parameter List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'. http://purl.obolibrary.org/obo/MS_1001761 ACQUITY UPLC http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters LC-system ACQUITY UPLC. http://purl.obolibrary.org/obo/MS_1001762 ACQUITY UPLC H-Class http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters LC-system ACQUITY UPLC H-Class. http://purl.obolibrary.org/obo/MS_1001763 ACQUITY UPLC H-Class Bio http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters LC-system ACQUITY UPLC H-Class Bio. http://purl.obolibrary.org/obo/MS_1001764 ACQUITY UPLC I-Class http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters LC-system ACQUITY UPLC I-Class. http://purl.obolibrary.org/obo/MS_1001765 ACQUITY UPLC Systems with 2D Technology http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters LC-system ACQUITY UPLC Systems with 2D Technology. http://purl.obolibrary.org/obo/MS_1001766 nanoACQUITY UPLC http://purl.obolibrary.org/obo/MS_1003599 nano-flow liquid chromatography system Waters LC-system nanoACQUITY UPLC. http://purl.obolibrary.org/obo/MS_1001767 nanoACQUITY UPLC System with 1D Technology http://purl.obolibrary.org/obo/MS_1003599 nano-flow liquid chromatography system Waters LC-system nanoACQUITY UPLC System with 1D Technology. http://purl.obolibrary.org/obo/MS_1001768 nanoACQUITY UPLC with HDX Technology http://purl.obolibrary.org/obo/MS_1003599 nano-flow liquid chromatography system Waters LC-system nanoACQUITY UPLC with HDX Technology. http://purl.obolibrary.org/obo/MS_1001769 TRIZAIC UPLC nanoTile http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters LC-system TRIZAIC UPLC nanoTile. http://purl.obolibrary.org/obo/MS_1001770 GCT Premier http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Waters oa-ToF based GCT Premier. http://purl.obolibrary.org/obo/MS_1001771 MALDI Synapt G2 HDMS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters oa-ToF based MALDI Synapt G2 HDMS. http://purl.obolibrary.org/obo/MS_1001772 MALDI Synapt G2 MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based MALDI Synapt G2 MS. http://purl.obolibrary.org/obo/MS_1001773 MALDI Synapt G2-S HDMS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters oa-ToF based MALDI Synapt G2 MS. http://purl.obolibrary.org/obo/MS_1001774 MALDI Synapt G2-S MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based MALDI Synapt G2-S MS. http://purl.obolibrary.org/obo/MS_1001775 MALDI Synapt HDMS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters oa-ToF based MALDI Synapt HDMS. http://purl.obolibrary.org/obo/MS_1001776 MALDI Synapt MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based MALDI Synapt MS. http://purl.obolibrary.org/obo/MS_1001777 Synapt G2 HDMS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters oa-ToF based Synapt G2 HDMS. http://purl.obolibrary.org/obo/MS_1001778 Synapt G2 MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based Synapt G2 MS. http://purl.obolibrary.org/obo/MS_1001779 Synapt G2-S HDMS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters oa-ToF based Synapt G2-S HDMS. http://purl.obolibrary.org/obo/MS_1001780 Synapt G2-S MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based Synapt G2-S MS. http://purl.obolibrary.org/obo/MS_1001781 Synapt HDMS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters oa-ToF based Synapt HDMS. http://purl.obolibrary.org/obo/MS_1001782 Synapt MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based Synapt MS. http://purl.obolibrary.org/obo/MS_1001783 Xevo G2 Q-Tof http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based Xevo G2 Q-Tof. http://purl.obolibrary.org/obo/MS_1001784 Xevo G2 Tof http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Waters oa-ToF based Xevo G2 Tof. http://purl.obolibrary.org/obo/MS_1001785 Xevo Q-Tof http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based Xevo Q-Tof. http://purl.obolibrary.org/obo/MS_1001786 3100 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Waters quadrupole based 3100. http://purl.obolibrary.org/obo/MS_1001787 Acquity SQD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Waters quadrupole based Acquity SQD. http://purl.obolibrary.org/obo/MS_1001788 Acquity TQD http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters quadrupole based Acquity TQD. http://purl.obolibrary.org/obo/MS_1001789 Quattro micro GC http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters (triple) quadrupole based Quattro micro GC. http://purl.obolibrary.org/obo/MS_1001790 Xevo TQ MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters quadrupole based Xevo TQ MS. http://purl.obolibrary.org/obo/MS_1001791 Xevo TQD http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters quadrupole based Xevo TQD. http://purl.obolibrary.org/obo/MS_1001792 Xevo TQ-S http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters quadrupole based Xevo TQ-S. http://purl.obolibrary.org/obo/MS_1001793 Mascot:PreferredTaxonomy http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences. http://purl.obolibrary.org/obo/MS_1001795 Empower http://purl.obolibrary.org/obo/MS_1001457 data processing software Waters Empower software for liquid chromatography and mass spectrometry acquisition. http://purl.obolibrary.org/obo/MS_1001796 UNIFY http://purl.obolibrary.org/obo/MS_1001457 data processing software Waters UNIFY software for liquid chromatography and mass spectrometry acquisition. http://purl.obolibrary.org/obo/MS_1001798 LECO software http://purl.obolibrary.org/obo/MS_1000531 software LECO software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1001799 ChromaTOF software http://purl.obolibrary.org/obo/MS_1001798 LECO software Software for acquisition, processing and analysis of data for LECO instruments. http://purl.obolibrary.org/obo/MS_1001800 LECO instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model LECO instrument model. http://purl.obolibrary.org/obo/MS_1001801 Pegasus HRT http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO high resolution time-of-flight GC mass spectrometer. http://purl.obolibrary.org/obo/MS_1001802 Citius HRT http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO high resolution time-of-flight LC mass spectrometer. http://purl.obolibrary.org/obo/MS_1001803 Pegasus http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO GC time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1001804 TruTOF http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO bench-top GC time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1001805 quantification datatype http://purl.obolibrary.org/obo/MS_1001129 quantification information The data type of the value reported in a QuantLayer. http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute http://purl.obolibrary.org/obo/MS_1001129 quantification information Attributes describing the details of an object relevant for reporting quantification workflows or values. http://purl.obolibrary.org/obo/MS_1001807 study variable attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a study variable. http://purl.obolibrary.org/obo/MS_1001808 technical replicate http://purl.obolibrary.org/obo/MS_1001807 study variable attribute The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'. http://purl.obolibrary.org/obo/MS_1001809 biological replicate http://purl.obolibrary.org/obo/MS_1001807 study variable attribute The study variable is 'biological replicate'. This means, the run was generated from another individual or sample. http://purl.obolibrary.org/obo/MS_1001810 experimental condition 'case' http://purl.obolibrary.org/obo/MS_1001807 study variable attribute The experimental condition is 'case' in contrast to 'control'. http://purl.obolibrary.org/obo/MS_1001811 experimental condition 'control' http://purl.obolibrary.org/obo/MS_1001807 study variable attribute The experimental condition is 'control' in contrast to 'case'. http://purl.obolibrary.org/obo/MS_1001812 experimental condition 'disease' http://purl.obolibrary.org/obo/MS_1001807 study variable attribute The experimental condition is 'disease' in contrast to 'healthy'. http://purl.obolibrary.org/obo/MS_1001813 experimental condition 'healthy' http://purl.obolibrary.org/obo/MS_1001807 study variable attribute The experimental condition is 'healthy' in contrast to 'disease'. http://purl.obolibrary.org/obo/MS_1001814 generic experimental condition http://purl.obolibrary.org/obo/MS_1001807 study variable attribute The experimental condition is given in the value of this term. http://purl.obolibrary.org/obo/MS_1001815 time series, time point X http://purl.obolibrary.org/obo/MS_1001807 study variable attribute The experimental design followed a time series design. The time point of this run is given in the value of this term. http://purl.obolibrary.org/obo/MS_1001816 dilution series, concentration X http://purl.obolibrary.org/obo/MS_1001807 study variable attribute The experimental design followed a dilution series design. The concentration of this run is given in the value of this term. http://purl.obolibrary.org/obo/MS_1001817 raw file attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a raw file. http://purl.obolibrary.org/obo/MS_1001818 one sample run http://purl.obolibrary.org/obo/MS_1001817 raw file attribute The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free). http://purl.obolibrary.org/obo/MS_1001819 two sample run http://purl.obolibrary.org/obo/MS_1001817 raw file attribute The raw file contains the run of two samples (e.g. SILAC, metabolic labelling). http://purl.obolibrary.org/obo/MS_1001820 three sample run http://purl.obolibrary.org/obo/MS_1001817 raw file attribute The raw file contains the run of three samples (e.g. 3-plex SILAC). http://purl.obolibrary.org/obo/MS_1001821 four sample run http://purl.obolibrary.org/obo/MS_1001817 raw file attribute The raw file contains the run of four samples (e.g. 4-plex iTraq). http://purl.obolibrary.org/obo/MS_1001822 eight sample run http://purl.obolibrary.org/obo/MS_1001817 raw file attribute The raw file contains the run of eight samples (e.g. 8-plex iTraq). http://purl.obolibrary.org/obo/MS_1001823 raw files group attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing, how raw files build a raw file group. http://purl.obolibrary.org/obo/MS_1001824 merge of runs of 1D gel bands http://purl.obolibrary.org/obo/MS_1001823 raw files group attribute Attribute describing, how raw files build a raw file group. http://purl.obolibrary.org/obo/MS_1001825 feature list attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a feature list. http://purl.obolibrary.org/obo/MS_1001826 mass trace reporting: rectangles http://purl.obolibrary.org/obo/MS_1001825 feature list attribute The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given. http://purl.obolibrary.org/obo/MS_1001827 mass trace reporting: polygons http://purl.obolibrary.org/obo/MS_1001825 feature list attribute The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, ... , RT_i, MZ_i, ... , RT_n, MZ_n), where the line (RT_n, MZ_n)->(RT_1, MZ_1) is implicit. http://purl.obolibrary.org/obo/MS_1001828 feature attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a feature. http://purl.obolibrary.org/obo/MS_1001829 SRM transition ID http://purl.obolibrary.org/obo/MS_1001828 feature attribute Identifier for an SRM transition in an external document describing additional information about the transition. http://purl.obolibrary.org/obo/MS_1001830 Progenesis LC-MS http://purl.obolibrary.org/obo/MS_1001139 quantitation software name Software from Nonlinear Dynamics for LC-MS label-free workflow. http://purl.obolibrary.org/obo/MS_1001831 SILACAnalyzer http://purl.obolibrary.org/obo/MS_1001139 quantitation software name Software for SILAC workflow. http://purl.obolibrary.org/obo/MS_1001832 quantitation software comment or customizations http://purl.obolibrary.org/obo/MS_1001129 quantification information Quantitation software comment or any customizations to the default setup of the software. http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary http://purl.obolibrary.org/obo/MS_1001129 quantification information The overall workflow of this quantitation report. http://purl.obolibrary.org/obo/MS_1001834 LC-MS label-free quantitation analysis http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary LC-MS label-free workflow (RT m/z map). http://purl.obolibrary.org/obo/MS_1001835 SILAC quantitation analysis http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary SILAC workflow (heavy, light, and sometimes medium peak). http://purl.obolibrary.org/obo/MS_1001836 spectral counting quantitation analysis http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant). http://purl.obolibrary.org/obo/MS_1001837 iTRAQ quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range. http://purl.obolibrary.org/obo/MS_1001838 SRM quantitation analysis http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). http://purl.obolibrary.org/obo/MS_1001839 metabolic labeling 14N / 15N quantitation analysis http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens). http://purl.obolibrary.org/obo/MS_1001840 LC-MS feature intensity http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype Maximum peak intensity of the LC-MS feature. http://purl.obolibrary.org/obo/MS_1001841 LC-MS feature volume http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype Real (intensity times area) volume of the LC-MS feature. http://purl.obolibrary.org/obo/MS_1001842 sequence-level spectral count http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting. http://purl.obolibrary.org/obo/MS_1001843 MS1 feature maximum intensity http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype Maximum intensity of MS1 feature. http://purl.obolibrary.org/obo/MS_1001844 MS1 feature area http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype Area of MS1 feature. http://purl.obolibrary.org/obo/MS_1001845 peak area http://purl.obolibrary.org/obo/MS_1001805 quantification datatype OBSOLETE Area of MS1 peak (e.g. SILAC, 15N). http://purl.obolibrary.org/obo/MS_1001846 isotopic pattern area http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N). http://purl.obolibrary.org/obo/MS_1001847 reporter ion intensity http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Intensity of MS2 reporter ion (e.g. iTraq). http://purl.obolibrary.org/obo/MS_1001848 simple ratio of two values http://purl.obolibrary.org/obo/MS_1002066 ratio calculation method Simple ratio of two values (enumerator and denominator). http://purl.obolibrary.org/obo/MS_1001849 sum of MatchedFeature values http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values. http://purl.obolibrary.org/obo/MS_1001850 normalized peptide value http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype Normalized peptide value. http://purl.obolibrary.org/obo/MS_1001851 protein value: sum of peptide values http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype Protein quantification value calculated as sum of peptide values. http://purl.obolibrary.org/obo/MS_1001852 normalized protein value http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype Normalized protein value. http://purl.obolibrary.org/obo/MS_1001853 max fold change http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis). http://purl.obolibrary.org/obo/MS_1001854 ANOVA p-value http://purl.obolibrary.org/obo/MS_1002072 p-value Global datatype: p-value of ANOVA of group means (e.g. Progenesis). http://purl.obolibrary.org/obo/MS_1001855 t-test p-value http://purl.obolibrary.org/obo/MS_1002072 p-value P-value of t-Test of two groups. http://purl.obolibrary.org/obo/MS_1001856 reporter ion raw value http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Intensity (or area) of MS2 reporter ion (e.g. iTraq). http://purl.obolibrary.org/obo/MS_1001857 reporter ion normalized value http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Normalized value of MS2 reporter ion (e.g. iTraq). http://purl.obolibrary.org/obo/MS_1001858 XIC area http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Area of the extracted ion chromatogram (e.g. of a transition in SRM). http://purl.obolibrary.org/obo/MS_1001859 normalized XIC area http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM). http://purl.obolibrary.org/obo/MS_1001860 protein value: mean of peptide ratios http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype Protein quantification value calculated as mean of peptide ratios. http://purl.obolibrary.org/obo/MS_1001862 normalization to mean of sum of all proteins http://purl.obolibrary.org/obo/MS_1001861 quantification data processing Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting). http://purl.obolibrary.org/obo/MS_1001863 quantile normalization, proteins http://purl.obolibrary.org/obo/MS_1001861 quantification data processing Normalization of protein values to approach the same distribution. http://purl.obolibrary.org/obo/MS_1001864 quantile normalization, peptides http://purl.obolibrary.org/obo/MS_1001861 quantification data processing Normalization of peptide values to approach the same distribution. http://purl.obolibrary.org/obo/MS_1001865 Progenesis automatic alignment http://purl.obolibrary.org/obo/MS_1001861 quantification data processing Automatic RT alignment of Progenesis software. http://purl.obolibrary.org/obo/MS_1001866 Progenesis manual alignment http://purl.obolibrary.org/obo/MS_1001861 quantification data processing RT alignment of Progenesis software using automatic and manual vectors. http://purl.obolibrary.org/obo/MS_1001867 Progenesis normalization http://purl.obolibrary.org/obo/MS_1001861 quantification data processing Normalization as performed by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1001868 distinct peptide-level q-value http://purl.obolibrary.org/obo/MS_1002484 peptide-level statistical threshold Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry). http://purl.obolibrary.org/obo/MS_1001869 protein-level q-value http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Estimation of the q-value for proteins. http://purl.obolibrary.org/obo/MS_1001870 peptide sequence-level p-value http://purl.obolibrary.org/obo/MS_1001092 peptide sequence-level identification statistic Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). http://purl.obolibrary.org/obo/MS_1001871 protein-level p-value http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Estimation of the p-value for proteins. http://purl.obolibrary.org/obo/MS_1001872 peptide sequence-level e-value http://purl.obolibrary.org/obo/MS_1001092 peptide sequence-level identification statistic Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). http://purl.obolibrary.org/obo/MS_1001873 protein-level e-value http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Estimation of the e-value for proteins. http://purl.obolibrary.org/obo/MS_1001874 FDRScore http://purl.obolibrary.org/obo/MS_1001153 search engine specific score OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0. http://purl.obolibrary.org/obo/MS_1001875 modification motif http://purl.obolibrary.org/obo/MS_1001056 modification specificity rule The regular expression describing the sequence motif for a modification. http://purl.obolibrary.org/obo/MS_1001876 modification probability http://purl.obolibrary.org/obo/MS_1001056 modification specificity rule The a priori probability of a modification. http://purl.obolibrary.org/obo/MS_1001877 ChromaTOF HRT software http://purl.obolibrary.org/obo/MS_1001798 LECO software Software for acquisition, processing and analysis of data for LECO instruments. http://purl.obolibrary.org/obo/MS_1001878 MALDI Solutions Microbial Identification http://purl.obolibrary.org/obo/MS_1001558 MALDI Solutions Shimadzu Biotech software for data acquisition, processing, and analysis. http://purl.obolibrary.org/obo/MS_1001879 source offset voltage http://purl.obolibrary.org/obo/MS_1000503 scan attribute The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation. http://purl.obolibrary.org/obo/MS_1001880 in-source collision-induced dissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum. http://purl.obolibrary.org/obo/MS_1001881 mz5 format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format mz5 file format, modelled after mzML. http://purl.obolibrary.org/obo/MS_1001883 coefficient of variation http://purl.obolibrary.org/obo/MS_1001882 transition validation attribute Variation of a set of signal measurements calculated as the standard deviation relative to the mean. http://purl.obolibrary.org/obo/MS_1001884 signal-to-noise ratio http://purl.obolibrary.org/obo/MS_1001882 transition validation attribute Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal. http://purl.obolibrary.org/obo/MS_1001885 command-line parameters http://purl.obolibrary.org/obo/MS_1003201 library provenance attribute Parameters string passed to a command-line interface software application, omitting the executable name. http://purl.obolibrary.org/obo/MS_1001886 SQID http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for data analysis of peptides and proteins. http://purl.obolibrary.org/obo/MS_1001887 SQID:score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SQID result 'Score'. http://purl.obolibrary.org/obo/MS_1001888 SQID:deltaScore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SQID result 'deltaScore'. http://purl.obolibrary.org/obo/MS_1001889 SQID:protein score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The SQID result 'protein score'. http://purl.obolibrary.org/obo/MS_1001890 Progenesis:protein normalised abundance http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype The data type normalised abundance for proteins produced by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1001891 Progenesis:peptide normalised abundance http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The data type normalised abundance for peptides produced by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1001892 Progenesis:protein raw abundance http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype The data type raw abundance for proteins produced by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1001893 Progenesis:peptide raw abundance http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The data type raw abundance for peptide produced by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1001894 Progenesis:confidence score http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type confidence score produced by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1001895 Progenesis:peptide count http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The data type peptide count produced by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1001896 Progenesis:feature intensity http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype The data type feature intensity produced by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1001897 MaxQuant:peptide counts (unique) http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The data type peptide counts (unique) produced by MaxQuant. http://purl.obolibrary.org/obo/MS_1001898 MaxQuant:peptide counts (all) http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The data type peptide counts (all) produced by MaxQuant. http://purl.obolibrary.org/obo/MS_1001899 MaxQuant:peptide counts (razor+unique) http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The data type peptide counts (razor+unique) produced by MaxQuant. http://purl.obolibrary.org/obo/MS_1001900 MaxQuant:sequence length http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The data type sequence length produced by MaxQuant. http://purl.obolibrary.org/obo/MS_1001901 MaxQuant:PEP http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type PEP (posterior error probability) produced by MaxQuant. http://purl.obolibrary.org/obo/MS_1001902 MaxQuant:LFQ intensity http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type LFQ intensity produced by MaxQuant. http://purl.obolibrary.org/obo/MS_1001903 MaxQuant:feature intensity http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype The data type feature intensity produced by MaxQuant. http://purl.obolibrary.org/obo/MS_1001904 MaxQuant:MS/MS count http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type MS2 count produced by MaxQuant. http://purl.obolibrary.org/obo/MS_1001905 emPAI value http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype The emPAI value of protein abundance, produced from the emPAI algorithm. http://purl.obolibrary.org/obo/MS_1001906 APEX value http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype The APEX value of protein abundance, produced from the APEX software. http://purl.obolibrary.org/obo/MS_1001907 retention time window width http://purl.obolibrary.org/obo/MS_1000915 retention time window attribute The full width of a retention time window for a chromatographic peak. http://purl.obolibrary.org/obo/MS_1001908 ISQ http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source. http://purl.obolibrary.org/obo/MS_1001909 Velos Plus http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Scientific second generation Velos. http://purl.obolibrary.org/obo/MS_1001910 Orbitrap Elite http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Thermo Scientific Orbitrap Elite, sometimes referred to as the LTQ Orbitrap Elite. http://purl.obolibrary.org/obo/MS_1001911 Q Exactive http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Q Exactive. http://purl.obolibrary.org/obo/MS_1001912 PinPoint http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific PinPoint SRM analysis software. http://purl.obolibrary.org/obo/MS_1001913 S-lens voltage http://purl.obolibrary.org/obo/MS_1000482 source attribute Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts. http://purl.obolibrary.org/obo/MS_1001914 pymzML http://purl.obolibrary.org/obo/MS_1001457 data processing software Python module to interface mzML Data. http://purl.obolibrary.org/obo/MS_1001915 leukocyte elastase http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Enzyme leukocyte elastase (EC 3.4.21.37). http://purl.obolibrary.org/obo/MS_1001916 proline endopeptidase http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Enzyme proline endopeptidase (EC 3.4.21.26). http://purl.obolibrary.org/obo/MS_1001917 glutamyl endopeptidase http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Enzyme glutamyl endopeptidase (EC 3.4.21.19). http://purl.obolibrary.org/obo/MS_1001918 2-iodobenzoate http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Chemical iodobenzoate. Cleaves after W. http://purl.obolibrary.org/obo/MS_1001919 ProteomeXchange accession number http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Main identifier of a ProteomeXchange dataset. http://purl.obolibrary.org/obo/MS_1001921 ProteomeXchange accession number version number http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Version number of a ProteomeXchange accession number. http://purl.obolibrary.org/obo/MS_1001922 Digital Object Identifier (DOI) http://purl.obolibrary.org/obo/MS_1000878 external reference identifier DOI unique identifier of a publication. http://purl.obolibrary.org/obo/MS_1001923 external reference keyword http://purl.obolibrary.org/obo/MS_1002840 external reference data Free text attribute that can enrich the information about an entity. http://purl.obolibrary.org/obo/MS_1001924 journal article keyword http://purl.obolibrary.org/obo/MS_1001923 external reference keyword Keyword present in a scientific publication. http://purl.obolibrary.org/obo/MS_1001925 submitter keyword http://purl.obolibrary.org/obo/MS_1001923 external reference keyword Keyword assigned by the data submitter. http://purl.obolibrary.org/obo/MS_1001926 curator keyword http://purl.obolibrary.org/obo/MS_1001923 external reference keyword Keyword assigned by a data curator. http://purl.obolibrary.org/obo/MS_1001927 Tranche file hash http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Hash assigned by the Tranche resource to an individual file. http://purl.obolibrary.org/obo/MS_1001928 Tranche project hash http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Hash assigned by the Tranche resource to a whole project. http://purl.obolibrary.org/obo/MS_1001929 PRIDE experiment URI http://purl.obolibrary.org/obo/MS_1000878 external reference identifier URI that allows the access to one experiment in the PRIDE database. http://purl.obolibrary.org/obo/MS_1001930 PRIDE project URI http://purl.obolibrary.org/obo/MS_1000878 external reference identifier URI that allows the access to one project in the PRIDE database. http://purl.obolibrary.org/obo/MS_1001939 stainless steel plate http://purl.obolibrary.org/obo/MS_1001938 sample plate type Stainless steel plate. http://purl.obolibrary.org/obo/MS_1001940 coated glass plate http://purl.obolibrary.org/obo/MS_1001938 sample plate type Coated glass plate. http://purl.obolibrary.org/obo/MS_1001942 static supply electrospray http://purl.obolibrary.org/obo/MS_1001941 electrospray supply type The sprayer is loaded with sample once. http://purl.obolibrary.org/obo/MS_1001943 fed supply electrospray http://purl.obolibrary.org/obo/MS_1001941 electrospray supply type The sprayer is continuously fed with sample. http://purl.obolibrary.org/obo/MS_1001944 Collision cell exit potential http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts. http://purl.obolibrary.org/obo/MS_1001945 Pegasus 4D http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO nominal mass resolution time-of-flight GCxGC mass spectrometer. http://purl.obolibrary.org/obo/MS_1001946 PEAKS Studio http://purl.obolibrary.org/obo/MS_1001457 data processing software PEAKS Studio software for data analysis. http://purl.obolibrary.org/obo/MS_1001947 PEAKS Online http://purl.obolibrary.org/obo/MS_1001457 data processing software PEAKS Online software for high throughput data analysis. http://purl.obolibrary.org/obo/MS_1001948 PEAKS Node http://purl.obolibrary.org/obo/MS_1001457 data processing software PEAKS Node software for high throughput data analysis. http://purl.obolibrary.org/obo/MS_1001949 BSI software http://purl.obolibrary.org/obo/MS_1000531 software Bioinformatics Solutions Inc. Software for data processing and analysis. http://purl.obolibrary.org/obo/MS_1001950 PEAKS:peptideScore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The PEAKS peptide '-10lgP Score'. http://purl.obolibrary.org/obo/MS_1001951 PEAKS:proteinScore http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The PEAKS protein '-10lgP Score'. http://purl.obolibrary.org/obo/MS_1001952 ZCore:probScore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The ZCore probability score. http://purl.obolibrary.org/obo/MS_1001955 no cleavage http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name No cleavage. http://purl.obolibrary.org/obo/MS_1001956 unspecific cleavage http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Unspecific cleavage. http://purl.obolibrary.org/obo/MS_1001957 (?<=[ALIV])(? http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for leukocyte elastase. http://purl.obolibrary.org/obo/MS_1001958 (?<=[HKR]P)(? http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for proline endopeptidase. http://purl.obolibrary.org/obo/MS_1001959 (?<=[^E]E) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for glutamyl endopeptidase. http://purl.obolibrary.org/obo/MS_1001960 (?<=W) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for 2-iodobenzoate. http://purl.obolibrary.org/obo/MS_1001962 Mascot:C13 counts http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter C13 peaks to use in peak detection. http://purl.obolibrary.org/obo/MS_1001963 ProteinExtractor:Weighting http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter Weighting factor for protein list compilation by ProteinExtractor. http://purl.obolibrary.org/obo/MS_1001964 ProteinScape:second round Mascot http://purl.obolibrary.org/obo/MS_1002100 ProteinScape input parameter Flag indicating a second round search with Mascot. http://purl.obolibrary.org/obo/MS_1001965 ProteinScape:second round Phenyx http://purl.obolibrary.org/obo/MS_1002100 ProteinScape input parameter Flag indicating a second round search with Phenyx. http://purl.obolibrary.org/obo/MS_1001966 product ion mobility http://purl.obolibrary.org/obo/MS_1001221 product ion attribute The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry. http://purl.obolibrary.org/obo/MS_1001967 product ion drift time http://purl.obolibrary.org/obo/MS_1002222 SRM transition attribute OBSOLETE The ion drift time of an MS2 product ion. http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic http://purl.obolibrary.org/obo/MS_1002689 PTM localization single result statistic Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level. http://purl.obolibrary.org/obo/MS_1001969 phosphoRS score http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic phosphoRS score for PTM site location at the PSM-level. http://purl.obolibrary.org/obo/MS_1001970 phosphoRS sequence probability http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic Probability that the respective isoform is correct. http://purl.obolibrary.org/obo/MS_1001971 phosphoRS site probability http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic Estimate of the probability that the respective site is truly phosphorylated. http://purl.obolibrary.org/obo/MS_1001972 PTM scoring algorithm version http://purl.obolibrary.org/obo/MS_1001471 peptide modification details Version of the post-translational modification scoring algorithm. http://purl.obolibrary.org/obo/MS_1001973 DeBunker http://purl.obolibrary.org/obo/MS_1001456 analysis software DeBunker software. http://purl.obolibrary.org/obo/MS_1001974 DeBunker:score http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic Score specific to DeBunker. http://purl.obolibrary.org/obo/MS_1001975 delta m/z http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value. http://purl.obolibrary.org/obo/MS_1001976 delta M http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value. http://purl.obolibrary.org/obo/MS_1001977 MSQuant http://purl.obolibrary.org/obo/MS_1001456 analysis software MSQuant software. http://purl.obolibrary.org/obo/MS_1001978 MSQuant:PTM-score http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic The PTM score from MSQuant software. http://purl.obolibrary.org/obo/MS_1001979 MaxQuant:PTM Score http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic The PTM score from MaxQuant software. http://purl.obolibrary.org/obo/MS_1001980 MaxQuant:Phospho (STY) Probabilities http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic The Phospho (STY) Probabilities from MaxQuant software. http://purl.obolibrary.org/obo/MS_1001981 MaxQuant:Phospho (STY) Score Diffs http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic The Phospho (STY) Score Diffs from MaxQuant software. http://purl.obolibrary.org/obo/MS_1001982 MaxQuant:P-site localization probability http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic The P-site localization probability value from MaxQuant software. http://purl.obolibrary.org/obo/MS_1001983 MaxQuant:PTM Delta Score http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest). http://purl.obolibrary.org/obo/MS_1001984 Ascore software http://purl.obolibrary.org/obo/MS_1001456 analysis software Ascore software. http://purl.obolibrary.org/obo/MS_1001985 Ascore http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic A-score for PTM site location at the PSM-level. http://purl.obolibrary.org/obo/MS_1001986 H-Score http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic H-Score for peptide phosphorylation site location. http://purl.obolibrary.org/obo/MS_1001987 vacuum drying MALDI sample preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Vacuum-drying MALDI sample preparation crystallization method. http://purl.obolibrary.org/obo/MS_1001988 crushed crystal MALDI sample preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Crushed-crystal MALDI sample preparation method. http://purl.obolibrary.org/obo/MS_1001989 fast evaporation MALDI sample preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Fast-evaporation MALDI sample preparation method. http://purl.obolibrary.org/obo/MS_1001990 overlayer MALDI sample preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Overlayer method combining features of the crushed-crystal method and the fast-evaporation method. http://purl.obolibrary.org/obo/MS_1001991 sandwich MALDI sample preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Sandwich MALDI sample preparation method. http://purl.obolibrary.org/obo/MS_1001992 spin coating MALDI sample preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Spin coating MALDI sample preparation method. http://purl.obolibrary.org/obo/MS_1001993 quick and dirty MALDI sample preparation http://purl.obolibrary.org/obo/MS_1000833 matrix application type Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling. http://purl.obolibrary.org/obo/MS_1001994 top hat baseline reduction http://purl.obolibrary.org/obo/MS_1000593 baseline reduction Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'. http://purl.obolibrary.org/obo/MS_1001995 convex hull baseline reduction http://purl.obolibrary.org/obo/MS_1000593 baseline reduction Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures. http://purl.obolibrary.org/obo/MS_1001996 median baseline reduction http://purl.obolibrary.org/obo/MS_1000593 baseline reduction The spectrum that will be baseline subtracted is divided into a number of segments. http://purl.obolibrary.org/obo/MS_1001997 wavelet transformation smoothing http://purl.obolibrary.org/obo/MS_1000592 smoothing The random noise is removed by using the undecimated wavelet transform. http://purl.obolibrary.org/obo/MS_1001998 sophisticated numerical annotation procedure http://purl.obolibrary.org/obo/MS_1000801 area peak picking It searches for known patterns in the measured spectrum. http://purl.obolibrary.org/obo/MS_1001999 area normalization http://purl.obolibrary.org/obo/MS_1001484 intensity normalization Normalization of areas below the curves. http://purl.obolibrary.org/obo/MS_1002000 LIFT http://purl.obolibrary.org/obo/MS_1000044 dissociation method A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID. http://purl.obolibrary.org/obo/MS_1002001 MS1 label-based raw feature quantitation http://purl.obolibrary.org/obo/MS_1002018 MS1 label-based analysis MS1 label-based raw feature quantitation. http://purl.obolibrary.org/obo/MS_1002002 MS1 label-based peptide level quantitation http://purl.obolibrary.org/obo/MS_1002018 MS1 label-based analysis MS1 label-based peptide level quantitation. http://purl.obolibrary.org/obo/MS_1002003 MS1 label-based protein level quantitation http://purl.obolibrary.org/obo/MS_1002018 MS1 label-based analysis MS1 label-based protein level quantitation. http://purl.obolibrary.org/obo/MS_1002004 MS1 label-based proteingroup level quantitation http://purl.obolibrary.org/obo/MS_1002018 MS1 label-based analysis MS1 label-based proteingroup level quantitation. http://purl.obolibrary.org/obo/MS_1002005 iRT retention time normalization standard http://purl.obolibrary.org/obo/MS_1000901 retention time normalization standard A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys. http://purl.obolibrary.org/obo/MS_1002007 target SRM transition http://purl.obolibrary.org/obo/MS_1002006 SRM transition type A transition used to target a specific compound that may be in the sample. http://purl.obolibrary.org/obo/MS_1002008 decoy SRM transition http://purl.obolibrary.org/obo/MS_1002006 SRM transition type A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows. http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary Quantitation analysis using an isobaric labelling workflow. http://purl.obolibrary.org/obo/MS_1002010 TMT quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z. http://purl.obolibrary.org/obo/MS_1002011 desorption electrospray ionization http://purl.obolibrary.org/obo/MS_1000240 atmospheric pressure ionization Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure. http://purl.obolibrary.org/obo/MS_1002012 Mascot:PTM site assignment confidence http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score). http://purl.obolibrary.org/obo/MS_1002013 collision energy ramp start http://purl.obolibrary.org/obo/MS_1000045 collision energy Collision energy at the start of the collision energy ramp. http://purl.obolibrary.org/obo/MS_1002014 collision energy ramp end http://purl.obolibrary.org/obo/MS_1000045 collision energy Collision energy at the end of the collision energy ramp. http://purl.obolibrary.org/obo/MS_1002015 spectral count peptide level quantitation http://purl.obolibrary.org/obo/MS_1001836 spectral counting quantitation analysis Spectral count peptide level quantitation. http://purl.obolibrary.org/obo/MS_1002016 spectral count protein level quantitation http://purl.obolibrary.org/obo/MS_1001836 spectral counting quantitation analysis Spectral count protein level quantitation. http://purl.obolibrary.org/obo/MS_1002017 spectral count proteingroup level quantitation http://purl.obolibrary.org/obo/MS_1001836 spectral counting quantitation analysis Spectral count proteingroup level quantitation. http://purl.obolibrary.org/obo/MS_1002018 MS1 label-based analysis http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary MS1 label-based analysis. http://purl.obolibrary.org/obo/MS_1002019 label-free raw feature quantitation http://purl.obolibrary.org/obo/MS_1001834 LC-MS label-free quantitation analysis Label-free raw feature quantitation. http://purl.obolibrary.org/obo/MS_1002020 label-free peptide level quantitation http://purl.obolibrary.org/obo/MS_1001834 LC-MS label-free quantitation analysis Label-free peptide level quantitation. http://purl.obolibrary.org/obo/MS_1002021 label-free protein level quantitation http://purl.obolibrary.org/obo/MS_1001834 LC-MS label-free quantitation analysis Label-free protein level quantitation. http://purl.obolibrary.org/obo/MS_1002022 label-free proteingroup level quantitation http://purl.obolibrary.org/obo/MS_1001834 LC-MS label-free quantitation analysis Label-free proteingroup level quantitation. http://purl.obolibrary.org/obo/MS_1002023 MS2 tag-based analysis http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary MS2 tag-based analysis. http://purl.obolibrary.org/obo/MS_1002024 MS2 tag-based feature level quantitation http://purl.obolibrary.org/obo/MS_1002023 MS2 tag-based analysis MS2 tag-based feature level quantitation. http://purl.obolibrary.org/obo/MS_1002025 MS2 tag-based peptide level quantitation http://purl.obolibrary.org/obo/MS_1002023 MS2 tag-based analysis MS2 tag-based peptide level quantitation. http://purl.obolibrary.org/obo/MS_1002026 MS2 tag-based protein level quantitation http://purl.obolibrary.org/obo/MS_1002023 MS2 tag-based analysis MS2 tag-based protein level quantitation. http://purl.obolibrary.org/obo/MS_1002027 MS2 tag-based proteingroup level quantitation http://purl.obolibrary.org/obo/MS_1002023 MS2 tag-based analysis MS2 tag-based proteingroup level quantitation. http://purl.obolibrary.org/obo/MS_1002028 nucleic acid base modification http://purl.obolibrary.org/obo/MS_1001471 peptide modification details Nucleic acid base modification (substitution, insertion or deletion). http://purl.obolibrary.org/obo/MS_1002029 original nucleic acid sequence http://purl.obolibrary.org/obo/MS_1001471 peptide modification details Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence. http://purl.obolibrary.org/obo/MS_1002030 modified nucleic acid sequence http://purl.obolibrary.org/obo/MS_1001471 peptide modification details Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence. http://purl.obolibrary.org/obo/MS_1002031 PASSEL transition group browser URI http://purl.obolibrary.org/obo/MS_1000878 external reference identifier URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment. http://purl.obolibrary.org/obo/MS_1002032 PeptideAtlas dataset URI http://purl.obolibrary.org/obo/MS_1000878 external reference identifier URI that allows access to a PeptideAtlas dataset. http://purl.obolibrary.org/obo/MS_1002033 contact role http://purl.obolibrary.org/obo/MS_1000585 contact attribute Role of the contact person. http://purl.obolibrary.org/obo/MS_1002034 first author http://purl.obolibrary.org/obo/MS_1002033 contact role The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution. http://purl.obolibrary.org/obo/MS_1002035 senior author http://purl.obolibrary.org/obo/MS_1002033 contact role The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution. http://purl.obolibrary.org/obo/MS_1002036 co-author http://purl.obolibrary.org/obo/MS_1002033 contact role One of a set of authors associated with a publication or release. http://purl.obolibrary.org/obo/MS_1002037 dataset submitter http://purl.obolibrary.org/obo/MS_1002033 contact role A person who submits a dataset to a repository. http://purl.obolibrary.org/obo/MS_1002038 label free sample http://purl.obolibrary.org/obo/MS_1000548 sample attribute A sample that has not been labelled or modified. This is often referred to as "light" to distinguish from "heavy". http://purl.obolibrary.org/obo/MS_1002039 inlet attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute Inlet properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1002040 inlet temperature http://purl.obolibrary.org/obo/MS_1002039 inlet attribute The temperature of the inlet of a mass spectrometer. http://purl.obolibrary.org/obo/MS_1002041 source temperature http://purl.obolibrary.org/obo/MS_1000482 source attribute The temperature of the source of a mass spectrometer. http://purl.obolibrary.org/obo/MS_1002042 modulation time http://purl.obolibrary.org/obo/MS_1000857 run attribute The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column. http://purl.obolibrary.org/obo/MS_1002043 ProteinProspector http://purl.obolibrary.org/obo/MS_1001456 analysis software ProteinProspector software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1002044 ProteinProspector:score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The ProteinProspector result 'Score'. http://purl.obolibrary.org/obo/MS_1002045 ProteinProspector:expectation value http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The ProteinProspector result 'Expectation value'. http://purl.obolibrary.org/obo/MS_1002046 native source path http://purl.obolibrary.org/obo/MS_1001458 spectrum generation information The original source path used for directory-based sources. http://purl.obolibrary.org/obo/MS_1002047 MS-GF http://purl.obolibrary.org/obo/MS_1001456 analysis software MS-GF software used to re-score the peptide-spectrum matches. http://purl.obolibrary.org/obo/MS_1002048 MS-GF+ http://purl.obolibrary.org/obo/MS_1001456 analysis software MS-GF+ software used to analyze the spectra. http://purl.obolibrary.org/obo/MS_1002049 MS-GF:RawScore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic MS-GF raw score. http://purl.obolibrary.org/obo/MS_1002050 MS-GF:DeNovoScore http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins MS-GF de novo score. http://purl.obolibrary.org/obo/MS_1002051 MS-GF:Energy http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic MS-GF energy score. http://purl.obolibrary.org/obo/MS_1002052 MS-GF:SpecEValue http://purl.obolibrary.org/obo/MS_1002353 PSM-level e-value MS-GF spectral E-value. http://purl.obolibrary.org/obo/MS_1002053 MS-GF:EValue http://purl.obolibrary.org/obo/MS_1002353 PSM-level e-value MS-GF E-value. http://purl.obolibrary.org/obo/MS_1002054 MS-GF:QValue http://purl.obolibrary.org/obo/MS_1002354 PSM-level q-value MS-GF Q-value. http://purl.obolibrary.org/obo/MS_1002055 MS-GF:PepQValue http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic MS-GF peptide-level Q-value. http://purl.obolibrary.org/obo/MS_1002056 MS-GF:PEP http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic MS-GF posterior error probability. http://purl.obolibrary.org/obo/MS_1002057 modification specificity protein N-term http://purl.obolibrary.org/obo/MS_1001056 modification specificity rule As parameter for search engine: apply the modification only at the N-terminus of a protein. http://purl.obolibrary.org/obo/MS_1002058 modification specificity protein C-term http://purl.obolibrary.org/obo/MS_1001056 modification specificity rule As parameter for search engine: apply the modification only at the C-terminus of a protein. http://purl.obolibrary.org/obo/MS_1002059 Microsoft Excel http://purl.obolibrary.org/obo/MS_1001139 quantitation software name Microsoft Excel (can be used for spectral counting). http://purl.obolibrary.org/obo/MS_1002060 database UniProtKB/TrEMBL http://purl.obolibrary.org/obo/MS_1002126 database UniProtKB The name of the UniProtKB/TrEMBL database. http://purl.obolibrary.org/obo/MS_1002062 metabolic labelling: natural N (mainly 14N) http://purl.obolibrary.org/obo/MS_1001055 modification parameters Metabolic labelling: natural N (mainly 14N). http://purl.obolibrary.org/obo/MS_1002063 FindPairs http://purl.obolibrary.org/obo/MS_1001139 quantitation software name Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite. http://purl.obolibrary.org/obo/MS_1002064 peptide consensus RT http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype Peptide consensus retention time. http://purl.obolibrary.org/obo/MS_1002065 peptide consensus m/z http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype Peptide consensus mass/charge ratio. http://purl.obolibrary.org/obo/MS_1002066 ratio calculation method http://purl.obolibrary.org/obo/MS_1001805 quantification datatype Method used to calculate the ratio. http://purl.obolibrary.org/obo/MS_1002067 protein value: median of peptide ratios http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype Protein quantification value calculated as median of peptide ratios. http://purl.obolibrary.org/obo/MS_1002068 metabolic labelling: heavy N (mainly 15N) http://purl.obolibrary.org/obo/MS_1001055 modification parameters Metabolic labelling: heavy N (mainly 15N). http://purl.obolibrary.org/obo/MS_1002069 metabolic labelling purity http://purl.obolibrary.org/obo/MS_1001055 modification parameters Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape. http://purl.obolibrary.org/obo/MS_1002070 t-test http://purl.obolibrary.org/obo/MS_1001861 quantification data processing Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed. http://purl.obolibrary.org/obo/MS_1002071 ANOVA-test http://purl.obolibrary.org/obo/MS_1001861 quantification data processing Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed. http://purl.obolibrary.org/obo/MS_1002072 p-value http://purl.obolibrary.org/obo/MS_1001805 quantification datatype P-value as result of one of the processing steps described. Specify in the description, which processing step it was. http://purl.obolibrary.org/obo/MS_1002073 mzIdentML format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'. http://purl.obolibrary.org/obo/MS_1002074 quantification file format http://purl.obolibrary.org/obo/MS_1001459 file format File format containing quantification results. http://purl.obolibrary.org/obo/MS_1002075 mzQuantML format http://purl.obolibrary.org/obo/MS_1002074 quantification file format The mzQuantML format for quantification data from the PSI. File extension '.mzq'. http://purl.obolibrary.org/obo/MS_1002076 PAnalyzer http://purl.obolibrary.org/obo/MS_1001456 analysis software PAnalyzer software for getting protein evidence categories. http://purl.obolibrary.org/obo/MS_1002077 impact http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. http://purl.obolibrary.org/obo/MS_1002078 ProteomeDiscoverer:1. Static Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter. http://purl.obolibrary.org/obo/MS_1002079 ProteomeDiscoverer:2. Static Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter. http://purl.obolibrary.org/obo/MS_1002080 ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Precursor clipping range before. http://purl.obolibrary.org/obo/MS_1002081 ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Precursor clipping range after. http://purl.obolibrary.org/obo/MS_1002082 first column elution time http://purl.obolibrary.org/obo/MS_1000503 scan attribute The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column. http://purl.obolibrary.org/obo/MS_1002083 second column elution time http://purl.obolibrary.org/obo/MS_1000503 scan attribute The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column. http://purl.obolibrary.org/obo/MS_1002084 multidimensional chromatography modulation description http://purl.obolibrary.org/obo/MS_1000857 run attribute Multidimensional chromatography modulation description. http://purl.obolibrary.org/obo/MS_1002085 two-dimensional gas chromatography with fixed modulation time http://purl.obolibrary.org/obo/MS_1002084 multidimensional chromatography modulation description Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition. http://purl.obolibrary.org/obo/MS_1002086 two-dimensional gas chromatography with discrete modulation time steps http://purl.obolibrary.org/obo/MS_1002084 multidimensional chromatography modulation description Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time. http://purl.obolibrary.org/obo/MS_1002087 two-dimensional liquid chromatography with fixed modulation time http://purl.obolibrary.org/obo/MS_1002084 multidimensional chromatography modulation description Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition. http://purl.obolibrary.org/obo/MS_1002088 two-dimensional liquid chromatography with discrete modulation time steps http://purl.obolibrary.org/obo/MS_1002084 multidimensional chromatography modulation description Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time. http://purl.obolibrary.org/obo/MS_1002089 ProteomeDiscoverer:Peptide Without Protein XCorr Threshold http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter XCorr threshold for storing peptides that do not belong to a protein. http://purl.obolibrary.org/obo/MS_1002090 Calculate Probability Scores http://purl.obolibrary.org/obo/MS_1002094 common search engine input parameter Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated. http://purl.obolibrary.org/obo/MS_1002091 ProteomeDiscoverer:Maximum Delta Cn http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Delta Cn threshold for filtering out PSM's. http://purl.obolibrary.org/obo/MS_1002092 Percolator:Validation based on http://purl.obolibrary.org/obo/MS_1002107 Percolator input parameter Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator. http://purl.obolibrary.org/obo/MS_1002093 search engine input parameter http://purl.obolibrary.org/obo/MS_1001249 search input details Search engine input parameter. http://purl.obolibrary.org/obo/MS_1002094 common search engine input parameter http://purl.obolibrary.org/obo/MS_1002093 search engine input parameter Search engine input parameter that is shared by more than one search engine. http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to Mascot. http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to SEQUEST. http://purl.obolibrary.org/obo/MS_1002097 Phenyx input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to Phenyx. http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to ProteinExtractor. http://purl.obolibrary.org/obo/MS_1002099 OMSSA input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to OMSSA. http://purl.obolibrary.org/obo/MS_1002100 ProteinScape input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to ProteinScape. http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to ProteomeDiscoverer. http://purl.obolibrary.org/obo/MS_1002103 software input parameter http://purl.obolibrary.org/obo/MS_1001249 search input details Software input parameters. http://purl.obolibrary.org/obo/MS_1002104 common software input parameter http://purl.obolibrary.org/obo/MS_1002103 software input parameter Software input parameter that is shared by more than one software. http://purl.obolibrary.org/obo/MS_1002105 software specific input parameter http://purl.obolibrary.org/obo/MS_1002103 software input parameter Software specific input parameter. http://purl.obolibrary.org/obo/MS_1002106 Scaffold input parameter http://purl.obolibrary.org/obo/MS_1002105 software specific input parameter Search engine input parameters specific to Scaffold. http://purl.obolibrary.org/obo/MS_1002107 Percolator input parameter http://purl.obolibrary.org/obo/MS_1002105 software specific input parameter Search engine input parameters specific to Percolator. http://purl.obolibrary.org/obo/MS_1002110 assay attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing an assay. http://purl.obolibrary.org/obo/MS_1002111 assay label attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing an assay label. http://purl.obolibrary.org/obo/MS_1002112 protein group list attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a protein group list. http://purl.obolibrary.org/obo/MS_1002113 protein group attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a protein group. http://purl.obolibrary.org/obo/MS_1002114 protein list attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a protein list. http://purl.obolibrary.org/obo/MS_1002115 peptide consensus list attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a peptide consensus list. http://purl.obolibrary.org/obo/MS_1002116 peptide consensus attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a peptide consensus. http://purl.obolibrary.org/obo/MS_1002117 small molecule list attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a small molecule list. http://purl.obolibrary.org/obo/MS_1002118 small molecule attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a small molecule. http://purl.obolibrary.org/obo/MS_1002119 small molecule modification attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing a small molecule modification. http://purl.obolibrary.org/obo/MS_1002120 experiment name http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute The name for identifying an experiment. http://purl.obolibrary.org/obo/MS_1002121 spectral count feature http://purl.obolibrary.org/obo/MS_1001828 feature attribute Dummy describing a spectral count feature. http://purl.obolibrary.org/obo/MS_1002122 counts reporting http://purl.obolibrary.org/obo/MS_1001825 feature list attribute FeatureList of spectral counts. http://purl.obolibrary.org/obo/MS_1002123 x-Tracker http://purl.obolibrary.org/obo/MS_1001139 quantitation software name X-Tracker generic tool for quantitative proteomics. http://purl.obolibrary.org/obo/MS_1002124 ProteoSuite http://purl.obolibrary.org/obo/MS_1001139 quantitation software name ProteoSuite software for the analysis of quantitative proteomics data. http://purl.obolibrary.org/obo/MS_1002125 combined FDRScore http://purl.obolibrary.org/obo/MS_1001153 search engine specific score OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. http://purl.obolibrary.org/obo/MS_1002126 database UniProtKB http://purl.obolibrary.org/obo/MS_1001013 database name The name of the UniProtKB knowledgebase. http://purl.obolibrary.org/obo/MS_1002127 identification file attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing an identification file. http://purl.obolibrary.org/obo/MS_1002128 method file format http://purl.obolibrary.org/obo/MS_1001459 file format Attribute describing a method file format. http://purl.obolibrary.org/obo/MS_1002129 ITRAQAnalyzer http://purl.obolibrary.org/obo/MS_1001139 quantitation software name Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment. http://purl.obolibrary.org/obo/MS_1002130 identification file format http://purl.obolibrary.org/obo/MS_1001459 file format Attribute describing an identification file format. http://purl.obolibrary.org/obo/MS_1002131 TOPP noise filter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Noise filter component of the TOPP software. http://purl.obolibrary.org/obo/MS_1002132 TOPP NoiseFilterGaussian http://purl.obolibrary.org/obo/MS_1002131 TOPP noise filter Removes noise from profile spectra by using a gaussian smoothing. http://purl.obolibrary.org/obo/MS_1002133 TOPP NoiseFilterSGolay http://purl.obolibrary.org/obo/MS_1002131 TOPP noise filter Removes noise from profile spectra by using a Savitzky-Golay smoothing. http://purl.obolibrary.org/obo/MS_1002134 TOPP peak picker http://purl.obolibrary.org/obo/MS_1000752 TOPP software Peak picker component of the TOPP software. http://purl.obolibrary.org/obo/MS_1002135 TOPP PeakPickerHiRes http://purl.obolibrary.org/obo/MS_1002134 TOPP peak picker Finds mass spectrometric peaks in high-resoluted profile mass spectra. http://purl.obolibrary.org/obo/MS_1002136 TOPP PeakPickerWavelet http://purl.obolibrary.org/obo/MS_1002134 TOPP peak picker Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra. http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Spectra filter component of the TOPP software. http://purl.obolibrary.org/obo/MS_1002138 TOPP SpectraFilterBernNorm http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter Applies a Bern et al normalization to peak spectra. http://purl.obolibrary.org/obo/MS_1002139 TOPP SpectraFilterMarkerMower http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter Applies a filter to peak spectra for marked peaks. http://purl.obolibrary.org/obo/MS_1002140 TOPP SpectraFilterNLargest http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter Retains the n largest peaks of a peak spectra. http://purl.obolibrary.org/obo/MS_1002141 TOPP SpectraFilterNormalizer http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter Applies a TIC/maximal intensity normalization to peak spectra. http://purl.obolibrary.org/obo/MS_1002142 TOPP SpectraFilterParentPeakMower http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter Filters putative unfragmented precursor ions from tandem spectra. http://purl.obolibrary.org/obo/MS_1002143 TOPP SpectraFilterScaler http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter Applies a filter to peak spectra after intensity scaling according to rank. http://purl.obolibrary.org/obo/MS_1002144 TOPP SpectraFilterSqrtMower http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter Applies a filter to peak spectra after intensity scaling to the square root. http://purl.obolibrary.org/obo/MS_1002145 TOPP SpectraFilterThresholdMower http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter Applies a filter of peaks below a given threshold to peak spectra. http://purl.obolibrary.org/obo/MS_1002146 TOPP SpectraFilterWindowMower http://purl.obolibrary.org/obo/MS_1002137 TOPP spectra filter Applies a filter of the largest peaks in a sliding window over a peak spectrum. http://purl.obolibrary.org/obo/MS_1002147 TOPP map aligner http://purl.obolibrary.org/obo/MS_1000752 TOPP software Map aligner component of the TOPP software. http://purl.obolibrary.org/obo/MS_1002148 TOPP MapAlignerIdentification http://purl.obolibrary.org/obo/MS_1002147 TOPP map aligner Corrects retention time distortions between maps based on common peptide identifications. http://purl.obolibrary.org/obo/MS_1002149 TOPP MapAlignerPoseClustering http://purl.obolibrary.org/obo/MS_1002147 TOPP map aligner Corrects retention time distortions between maps using a pose clustering approach. http://purl.obolibrary.org/obo/MS_1002150 TOPP MapAlignerSpectrum http://purl.obolibrary.org/obo/MS_1002147 TOPP map aligner Corrects retention time distortions between maps by spectrum alignment. http://purl.obolibrary.org/obo/MS_1002151 numerator data type attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing the data type of the numerator of a ratio. http://purl.obolibrary.org/obo/MS_1002152 denominator data type attribute http://purl.obolibrary.org/obo/MS_1001806 quantification object attribute Attribute describing the data type of the denominator of a ratio. http://purl.obolibrary.org/obo/MS_1002153 protein level PSM counts http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype The number of spectra identified for this protein in spectral counting. http://purl.obolibrary.org/obo/MS_1002154 TOPP DTAExtractor http://purl.obolibrary.org/obo/MS_1000752 TOPP software Extracts spectra of an MS run file to several files in DTA format. http://purl.obolibrary.org/obo/MS_1002155 TOPP IDMerger http://purl.obolibrary.org/obo/MS_1000752 TOPP software Merges several protein/peptide identification files into one file. http://purl.obolibrary.org/obo/MS_1002156 TOPP IDFileConverter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Converts identification engine file formats. http://purl.obolibrary.org/obo/MS_1002157 TOPP SpectraMerger http://purl.obolibrary.org/obo/MS_1000752 TOPP software Merges spectra from an LC/MS map, either by precursor or by RT blocks. http://purl.obolibrary.org/obo/MS_1002158 TOPP MzTabExporter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Exports various XML formats to an mzTab file. http://purl.obolibrary.org/obo/MS_1002159 TOPP MassTraceExtractor http://purl.obolibrary.org/obo/MS_1000752 TOPP software Annotates mass traces in centroided LC/MS maps. http://purl.obolibrary.org/obo/MS_1002160 TOPP PrecursorMassCorrector http://purl.obolibrary.org/obo/MS_1000752 TOPP software Correct the precursor entries of tandem MS scans. http://purl.obolibrary.org/obo/MS_1002161 TOPP HighResPrecursorMassCorrector http://purl.obolibrary.org/obo/MS_1000752 TOPP software Performs precursor mz correction on centroided high resolution data. http://purl.obolibrary.org/obo/MS_1002162 TOPP AdditiveSeries http://purl.obolibrary.org/obo/MS_1000752 TOPP software Computes an additive series to quantify a peptide in a set of samples. http://purl.obolibrary.org/obo/MS_1002163 TOPP Decharger http://purl.obolibrary.org/obo/MS_1000752 TOPP software Decharges and merges different feature charge variants of the same chemical entity. http://purl.obolibrary.org/obo/MS_1002164 TOPP EICExtractor http://purl.obolibrary.org/obo/MS_1000752 TOPP software Quantifies signals at given positions in (raw or picked) LC/MS maps. http://purl.obolibrary.org/obo/MS_1002165 TOPP feature finder http://purl.obolibrary.org/obo/MS_1000752 TOPP software Feature finder component of the TOPP software. http://purl.obolibrary.org/obo/MS_1002166 TOPP FeatureFinderCentroided http://purl.obolibrary.org/obo/MS_1002165 TOPP feature finder Detects two-dimensional features in centroided LC-MS data. http://purl.obolibrary.org/obo/MS_1002167 TOPP FeatureFinderRaw http://purl.obolibrary.org/obo/MS_1002165 TOPP feature finder Detects two-dimensional features in uncentroided LC-MS data. http://purl.obolibrary.org/obo/MS_1002168 TOPP FeatureFinderIsotopeWavelet http://purl.obolibrary.org/obo/MS_1002165 TOPP feature finder Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm. http://purl.obolibrary.org/obo/MS_1002169 TOPP FeatureFinderMetabo http://purl.obolibrary.org/obo/MS_1002165 TOPP feature finder Detects two-dimensional features in centroided LC-MS data of metabolites. http://purl.obolibrary.org/obo/MS_1002170 TOPP FeatureFinderMRM http://purl.obolibrary.org/obo/MS_1002165 TOPP feature finder Quantifies features LC-MS/MS MRM data. http://purl.obolibrary.org/obo/MS_1002171 TOPP ProteinQuantifier http://purl.obolibrary.org/obo/MS_1000752 TOPP software Computes protein abundances from annotated feature/consensus maps. http://purl.obolibrary.org/obo/MS_1002172 TOPP ConsensusMapNormalizer http://purl.obolibrary.org/obo/MS_1000752 TOPP software Normalizes maps of one consensus XML file (after linking). http://purl.obolibrary.org/obo/MS_1002173 TOPP MapRTTransformer http://purl.obolibrary.org/obo/MS_1000752 TOPP software Applies retention time transformations to maps. http://purl.obolibrary.org/obo/MS_1002174 TOPP feature linker http://purl.obolibrary.org/obo/MS_1000752 TOPP software Feature linker component of the TOPP software. http://purl.obolibrary.org/obo/MS_1002175 TOPP FeatureLinkerLabeled http://purl.obolibrary.org/obo/MS_1002174 TOPP feature linker Groups corresponding isotope-labeled features in a feature map. http://purl.obolibrary.org/obo/MS_1002176 TOPP FeatureLinkerUnlabeled http://purl.obolibrary.org/obo/MS_1002174 TOPP feature linker Groups corresponding features from multiple maps. http://purl.obolibrary.org/obo/MS_1002177 TOPP FeatureLinkerUnlabeledQT http://purl.obolibrary.org/obo/MS_1002174 TOPP feature linker Groups corresponding features from multiple maps using a quality threshold clustering approach. http://purl.obolibrary.org/obo/MS_1002178 TOPP CompNovo http://purl.obolibrary.org/obo/MS_1000752 TOPP software Performs a peptide/protein identification with the CompNovo engine. http://purl.obolibrary.org/obo/MS_1002179 TOPP CompNovoCID http://purl.obolibrary.org/obo/MS_1000752 TOPP software Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode. http://purl.obolibrary.org/obo/MS_1002180 TOPP software adaptor http://purl.obolibrary.org/obo/MS_1000752 TOPP software Software adaptor to an external program in the TOPP software. http://purl.obolibrary.org/obo/MS_1002181 TOPP InspectAdapter http://purl.obolibrary.org/obo/MS_1002180 TOPP software adaptor Identifies MS2 spectra using the external program Inspect. http://purl.obolibrary.org/obo/MS_1002182 TOPP MascotAdapter http://purl.obolibrary.org/obo/MS_1002180 TOPP software adaptor Identifies MS2 spectra using the external program Mascot. http://purl.obolibrary.org/obo/MS_1002183 TOPP MascotAdapterOnline http://purl.obolibrary.org/obo/MS_1002180 TOPP software adaptor Identifies MS2 spectra using the online version of the external program Mascot. http://purl.obolibrary.org/obo/MS_1002184 TOPP OMSSAAdapter http://purl.obolibrary.org/obo/MS_1002180 TOPP software adaptor Identifies MS2 spectra using the external program OMSSA. http://purl.obolibrary.org/obo/MS_1002185 TOPP PepNovoAdapter http://purl.obolibrary.org/obo/MS_1002180 TOPP software adaptor Identifies MS2 spectra using the external program PepNovo. http://purl.obolibrary.org/obo/MS_1002186 TOPP XTandemAdapter http://purl.obolibrary.org/obo/MS_1002180 TOPP software adaptor Identifies MS2 spectra using the external program XTandem. http://purl.obolibrary.org/obo/MS_1002187 TOPP SpecLibSearcher http://purl.obolibrary.org/obo/MS_1000752 TOPP software Identifies peptide MS2 spectra by spectral matching with a searchable spectral library. http://purl.obolibrary.org/obo/MS_1002188 TOPP ConsensusID http://purl.obolibrary.org/obo/MS_1000752 TOPP software Computes a consensus identification from peptide identifications of several identification engines. http://purl.obolibrary.org/obo/MS_1002189 TOPP IDConflictResolver http://purl.obolibrary.org/obo/MS_1000752 TOPP software Resolves ambiguous annotations of features with peptide identifications. http://purl.obolibrary.org/obo/MS_1002190 TOPP IDFilter http://purl.obolibrary.org/obo/MS_1000752 TOPP software Filters results from protein or peptide identification engines based on different criteria. http://purl.obolibrary.org/obo/MS_1002191 TOPP IDMapper http://purl.obolibrary.org/obo/MS_1000752 TOPP software Assigns protein/peptide identifications to feature or consensus features. http://purl.obolibrary.org/obo/MS_1002192 TOPP IDPosteriorErrorProbability http://purl.obolibrary.org/obo/MS_1000752 TOPP software Estimates posterior error probabilities using a mixture model. http://purl.obolibrary.org/obo/MS_1002193 TOPP IDRTCalibration http://purl.obolibrary.org/obo/MS_1000752 TOPP software Calibrate Retention times of peptide hits to standards. http://purl.obolibrary.org/obo/MS_1002194 TOPP PeptideIndexer http://purl.obolibrary.org/obo/MS_1000752 TOPP software Refreshes the protein references for all peptide hits. http://purl.obolibrary.org/obo/MS_1002195 TOPP PrecursorIonSelector http://purl.obolibrary.org/obo/MS_1000752 TOPP software A tool for precursor ion selection based on identification results. http://purl.obolibrary.org/obo/MS_1002196 TOPP MRMMapper http://purl.obolibrary.org/obo/MS_1000752 TOPP software MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML). http://purl.obolibrary.org/obo/MS_1002197 TOPP OpenSwath component http://purl.obolibrary.org/obo/MS_1000752 TOPP software OpenSwath component of the TOPP software. http://purl.obolibrary.org/obo/MS_1002198 TOPP OpenSwathAnalyzer http://purl.obolibrary.org/obo/MS_1002197 TOPP OpenSwath component Picks peaks and finds features in an SRM experiment. http://purl.obolibrary.org/obo/MS_1002199 TOPP OpenSwathChromatogramExtractor http://purl.obolibrary.org/obo/MS_1002197 TOPP OpenSwath component Extract chromatograms (XIC) from a MS2 map file. http://purl.obolibrary.org/obo/MS_1002200 TOPP OpenSwathDecoyGenerator http://purl.obolibrary.org/obo/MS_1002197 TOPP OpenSwath component Generates decoys according to different models for a specific TraML. http://purl.obolibrary.org/obo/MS_1002201 TOPP OpenSwathFeatureXMLToTSV http://purl.obolibrary.org/obo/MS_1002197 TOPP OpenSwath component Converts a featureXML to a mProphet tsv (tab separated values). http://purl.obolibrary.org/obo/MS_1002202 TOPP OpenSwathRTNormalizer http://purl.obolibrary.org/obo/MS_1002197 TOPP OpenSwath component Generates a transformation file for retention time space into normalized space. http://purl.obolibrary.org/obo/MS_1002203 TOPP ProteinInference http://purl.obolibrary.org/obo/MS_1000752 TOPP software Infer proteins from a list of (high-confidence) peptides. http://purl.obolibrary.org/obo/MS_1002204 TOPP FalseDiscoveryRate http://purl.obolibrary.org/obo/MS_1000752 TOPP software Estimates the false discovery rate on peptide and protein level using decoy searches. http://purl.obolibrary.org/obo/MS_1002205 ProteoWizard msconvert http://purl.obolibrary.org/obo/MS_1000615 ProteoWizard software Converts, filters, and processes mass spectrometry data in variety of formats. http://purl.obolibrary.org/obo/MS_1002206 ProteoWizard idconvert http://purl.obolibrary.org/obo/MS_1000615 ProteoWizard software Converts, filters, and processes identifications from shotgun proteomics experiments. http://purl.obolibrary.org/obo/MS_1002207 ProteoWizard chainsaw http://purl.obolibrary.org/obo/MS_1000615 ProteoWizard software Filters and processes protein sequence databases. http://purl.obolibrary.org/obo/MS_1002208 ProteoWizard msaccess http://purl.obolibrary.org/obo/MS_1000615 ProteoWizard software Filters, processes, and displays mass spectrometry data in a variety of ways. http://purl.obolibrary.org/obo/MS_1002209 ProteoWizard SeeMS http://purl.obolibrary.org/obo/MS_1000615 ProteoWizard software An interactive GUI application to view and filter mass spectrometry data in a variety of formats. http://purl.obolibrary.org/obo/MS_1002210 IsobariQ http://purl.obolibrary.org/obo/MS_1001456 analysis software A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data. http://purl.obolibrary.org/obo/MS_1002211 Variance stabilizing normalization http://purl.obolibrary.org/obo/MS_1001861 quantification data processing The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. http://purl.obolibrary.org/obo/MS_1002212 IPTL quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric. http://purl.obolibrary.org/obo/MS_1002213 PAnalyzer:conclusive protein http://purl.obolibrary.org/obo/MS_1001600 protein inference confidence category A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum). http://purl.obolibrary.org/obo/MS_1002214 PAnalyzer:indistinguishable protein http://purl.obolibrary.org/obo/MS_1001600 protein inference confidence category A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum). http://purl.obolibrary.org/obo/MS_1002215 PAnalyzer:non-conclusive protein http://purl.obolibrary.org/obo/MS_1001600 protein inference confidence category A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). http://purl.obolibrary.org/obo/MS_1002216 PAnalyzer:ambiguous group member http://purl.obolibrary.org/obo/MS_1001600 protein inference confidence category A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). http://purl.obolibrary.org/obo/MS_1002217 decoy peptide http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute A putative identified peptide issued from a decoy sequence database. http://purl.obolibrary.org/obo/MS_1002218 percent collision energy ramp start http://purl.obolibrary.org/obo/MS_1000138 normalized collision energy Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion. http://purl.obolibrary.org/obo/MS_1002219 percent collision energy ramp end http://purl.obolibrary.org/obo/MS_1000138 normalized collision energy Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion. http://purl.obolibrary.org/obo/MS_1002220 MRMaid http://purl.obolibrary.org/obo/MS_1000871 SRM software A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database. http://purl.obolibrary.org/obo/MS_1002221 MRMaid:peptide score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins Score in MRMaid to indicate the expected performance of the peptide in SRM. http://purl.obolibrary.org/obo/MS_1002222 SRM transition attribute http://purl.obolibrary.org/obo/MS_1000455 ion selection attribute Attribute associated with a SRM transition. http://purl.obolibrary.org/obo/MS_1002223 precursor ion detection probability http://purl.obolibrary.org/obo/MS_1002222 SRM transition attribute Probability of detecting precursor when parent protein is present. http://purl.obolibrary.org/obo/MS_1002224 product ion detection probability http://purl.obolibrary.org/obo/MS_1002222 SRM transition attribute Probability of detecting product ion when precursor ion is present. http://purl.obolibrary.org/obo/MS_1002225 average product ion intensity http://purl.obolibrary.org/obo/MS_1001226 product ion intensity Average value of product ion intensity in a collection of identified spectra. http://purl.obolibrary.org/obo/MS_1002226 product ion intensity standard deviation http://purl.obolibrary.org/obo/MS_1001226 product ion intensity Standard deviation of product ion intensity in a collection of identified spectra. http://purl.obolibrary.org/obo/MS_1002227 number of product ion observations http://purl.obolibrary.org/obo/MS_1002222 SRM transition attribute The number of times the specific product ion has been observed in a series of SRM experiments. http://purl.obolibrary.org/obo/MS_1002228 number of precursor ion observations http://purl.obolibrary.org/obo/MS_1002222 SRM transition attribute The number of times the specific precursor ion has been observed in a series of SRM experiments. http://purl.obolibrary.org/obo/MS_1002229 ProteomeDiscoverer:Mascot:Significance Middle http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Calculated relaxed significance when performing a decoy search for high-confidence peptides. http://purl.obolibrary.org/obo/MS_1002230 ProteomeDiscoverer:Mascot:Significance High http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Calculated relaxed significance when performing a decoy search for medium-confidence peptides. http://purl.obolibrary.org/obo/MS_1002231 regular expressions for a GUID http://purl.obolibrary.org/obo/MS_1002479 regular expression ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12}). http://purl.obolibrary.org/obo/MS_1002232 ProteomeDiscoverer:Default FDR calculator http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter The default FDR calculator as globally unique identifier (GUID). http://purl.obolibrary.org/obo/MS_1002233 ProteomeDiscoverer:SEQUEST:Low resolution spectra contained http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Flag indicating if low-resolution spectra are taken into consideration. http://purl.obolibrary.org/obo/MS_1002234 selected precursor m/z http://purl.obolibrary.org/obo/MS_1000455 ion selection attribute Mass-to-charge ratio of a precursor ion selected for fragmentation. http://purl.obolibrary.org/obo/MS_1002235 ProteoGrouper:PDH score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores. http://purl.obolibrary.org/obo/MS_1002236 ProteoGrouper:PAG score http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides. http://purl.obolibrary.org/obo/MS_1002237 mzidLib http://purl.obolibrary.org/obo/MS_1001456 analysis software A library of Java routines for manipulating mzIdentML files. http://purl.obolibrary.org/obo/MS_1002238 mzidLib:Omssa2Mzid http://purl.obolibrary.org/obo/MS_1002237 mzidLib A converter for OMSSA OMX to mzIdentML. http://purl.obolibrary.org/obo/MS_1002239 mzidLib:Tandem2Mzid http://purl.obolibrary.org/obo/MS_1002237 mzidLib A converter for Tandem XML to mzIdentML. http://purl.obolibrary.org/obo/MS_1002240 mzidLib:Csv2Mzid http://purl.obolibrary.org/obo/MS_1002237 mzidLib A converter for CSV files (following OMSSA CSV style) to mzIdentML. http://purl.obolibrary.org/obo/MS_1002241 mzidLib:ProteoGrouper http://purl.obolibrary.org/obo/MS_1002237 mzidLib A generic and parameterizable protein inference algorithm for mzIdentML files. http://purl.obolibrary.org/obo/MS_1002242 mzidLib:Thresholder http://purl.obolibrary.org/obo/MS_1002237 mzidLib A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files. http://purl.obolibrary.org/obo/MS_1002243 mzidLib:Perform emPAI on mzid http://purl.obolibrary.org/obo/MS_1002237 mzidLib A routine for adding emPAI quantitative values to an mzIdentML file. http://purl.obolibrary.org/obo/MS_1002244 mzidLib:FalseDiscoveryRate http://purl.obolibrary.org/obo/MS_1002237 mzidLib A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search. http://purl.obolibrary.org/obo/MS_1002245 mzidLib:Mzidentml2Csv http://purl.obolibrary.org/obo/MS_1002237 mzidLib A tool for converting mzIdentML files to CSV format. http://purl.obolibrary.org/obo/MS_1002246 mzidLib:CombineSearchEngines http://purl.obolibrary.org/obo/MS_1002237 mzidLib A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file. http://purl.obolibrary.org/obo/MS_1002247 mzidLib:InsertMetaDataFromFasta http://purl.obolibrary.org/obo/MS_1002237 mzidLib A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files. http://purl.obolibrary.org/obo/MS_1002248 SEQUEST:spscore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'SpScore'. http://purl.obolibrary.org/obo/MS_1002249 SEQUEST:sprank http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'SpRank'. http://purl.obolibrary.org/obo/MS_1002250 SEQUEST:deltacnstar http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The SEQUEST result 'DeltaCnStar'. http://purl.obolibrary.org/obo/MS_1002251 Comet http://purl.obolibrary.org/obo/MS_1001456 analysis software Comet open-source sequence search engine developed at the University of Washington. http://purl.obolibrary.org/obo/MS_1002252 Comet:xcorr http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Comet result 'XCorr'. http://purl.obolibrary.org/obo/MS_1002253 Comet:deltacn http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Comet result 'DeltaCn'. http://purl.obolibrary.org/obo/MS_1002254 Comet:deltacnstar http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Comet result 'DeltaCnStar'. http://purl.obolibrary.org/obo/MS_1002255 Comet:spscore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Comet result 'SpScore'. http://purl.obolibrary.org/obo/MS_1002256 Comet:sprank http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Comet result 'SpRank'. http://purl.obolibrary.org/obo/MS_1002257 Comet:expectation value http://purl.obolibrary.org/obo/MS_1001153 search engine specific score The Comet result 'Expectation value'. http://purl.obolibrary.org/obo/MS_1002258 Comet:matched ions http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Comet result 'Matched Ions'. http://purl.obolibrary.org/obo/MS_1002259 Comet:total ions http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Comet result 'Total Ions'. http://purl.obolibrary.org/obo/MS_1002260 PSM:FDR threshold http://purl.obolibrary.org/obo/MS_1002483 PSM-level statistical threshold False-discovery rate threshold for peptide-spectrum matches. http://purl.obolibrary.org/obo/MS_1002261 Byonic http://purl.obolibrary.org/obo/MS_1001456 analysis software Byonic search engine from Protein Metrics. http://purl.obolibrary.org/obo/MS_1002262 Byonic:Score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct. http://purl.obolibrary.org/obo/MS_1002263 Byonic:Delta Score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct. http://purl.obolibrary.org/obo/MS_1002264 Byonic:DeltaMod Score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct. http://purl.obolibrary.org/obo/MS_1002265 Byonic:PEP http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Byonic posterior error probability. http://purl.obolibrary.org/obo/MS_1002266 Byonic:Peptide LogProb http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism. http://purl.obolibrary.org/obo/MS_1002267 Byonic:Protein LogProb http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The log p-value of the protein. http://purl.obolibrary.org/obo/MS_1002268 Byonic:Best LogProb http://purl.obolibrary.org/obo/MS_1001153 search engine specific score Best (most negative) log p-value of an individual PSM. http://purl.obolibrary.org/obo/MS_1002269 Byonic:Best Score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins Best (largest) Byonic score of a PSM. http://purl.obolibrary.org/obo/MS_1002270 chromatography separation http://purl.obolibrary.org/obo/MS_1000857 run attribute A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure. http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation http://purl.obolibrary.org/obo/MS_1002270 chromatography separation Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid. http://purl.obolibrary.org/obo/MS_1002272 gas chromatography separation http://purl.obolibrary.org/obo/MS_1002270 chromatography separation Gas chromatography (GC) is a separation technique in which the mobile phase is a gas. http://purl.obolibrary.org/obo/MS_1002273 detector potential http://purl.obolibrary.org/obo/MS_1000481 detector attribute Detector potential difference in volts. http://purl.obolibrary.org/obo/MS_1002274 SQ Detector 2 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Waters quadrupole based SQ Detector 2. http://purl.obolibrary.org/obo/MS_1002275 Xevo G2-S Tof http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Waters oa-ToF based Xevo G2-S Tof. http://purl.obolibrary.org/obo/MS_1002276 Xevo G2-S QTof http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based Xevo G2-S QTof. http://purl.obolibrary.org/obo/MS_1002277 AutoSpec Premier http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Waters AutoSpec Premier magnetic sector instrument. http://purl.obolibrary.org/obo/MS_1002278 Pegasus III http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO nominal mass resolution time-of-flight GC mass spectrometer. http://purl.obolibrary.org/obo/MS_1002279 maXis 4G http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. http://purl.obolibrary.org/obo/MS_1002280 compact http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. http://purl.obolibrary.org/obo/MS_1002281 SRM feature level quantitation http://purl.obolibrary.org/obo/MS_1001838 SRM quantitation analysis Selected Reaction Monitoring feature level quantitation. http://purl.obolibrary.org/obo/MS_1002282 SRM peptide level quantitation http://purl.obolibrary.org/obo/MS_1001838 SRM quantitation analysis Selected Reaction Monitoring peptide level quantitation. http://purl.obolibrary.org/obo/MS_1002283 SRM protein level quantitation http://purl.obolibrary.org/obo/MS_1001838 SRM quantitation analysis Selected Reaction Monitoring protein level quantitation. http://purl.obolibrary.org/obo/MS_1002284 SRM proteingroup level quantitation http://purl.obolibrary.org/obo/MS_1001838 SRM quantitation analysis Selected Reaction Monitoring proteingroup level quantitation. http://purl.obolibrary.org/obo/MS_1002285 Trans-Proteomic Pipeline http://purl.obolibrary.org/obo/MS_1001456 analysis software A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology. http://purl.obolibrary.org/obo/MS_1002286 Trans-Proteomic Pipeline software http://purl.obolibrary.org/obo/MS_1001456 analysis software A software program that is a component of the Trans-Proteomic Pipeline. http://purl.obolibrary.org/obo/MS_1002287 PeptideProphet http://purl.obolibrary.org/obo/MS_1002286 Trans-Proteomic Pipeline software A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format. http://purl.obolibrary.org/obo/MS_1002288 iProphet http://purl.obolibrary.org/obo/MS_1002286 Trans-Proteomic Pipeline software A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format. http://purl.obolibrary.org/obo/MS_1002289 ProteinProphet http://purl.obolibrary.org/obo/MS_1002286 Trans-Proteomic Pipeline software A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format. http://purl.obolibrary.org/obo/MS_1002290 XPRESS http://purl.obolibrary.org/obo/MS_1002286 Trans-Proteomic Pipeline software A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. http://purl.obolibrary.org/obo/MS_1002291 Libra http://purl.obolibrary.org/obo/MS_1002286 Trans-Proteomic Pipeline software A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc. http://purl.obolibrary.org/obo/MS_1002292 PTMProphet http://purl.obolibrary.org/obo/MS_1002286 Trans-Proteomic Pipeline software A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites. http://purl.obolibrary.org/obo/MS_1002293 Bruker Daltonics SCION series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' SCION series. http://purl.obolibrary.org/obo/MS_1002294 Bruker Daltonics EVOQ series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics' EVOQ series. http://purl.obolibrary.org/obo/MS_1002295 SCION SQ http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Bruker Daltonics' SCION SQ: GC-single quadrupole. http://purl.obolibrary.org/obo/MS_1002296 SCION TQ http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Bruker Daltonics' SCION TQ: GC-triple quadrupole. http://purl.obolibrary.org/obo/MS_1002297 EVOQ Elite http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Bruker Daltonics' EVOQ Elite: LC-triple quadrupole. http://purl.obolibrary.org/obo/MS_1002298 EVOQ Qube http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Bruker Daltonics' EVOQ Qube: LC-triple quadrupole. http://purl.obolibrary.org/obo/MS_1002299 micrOTOF-Q III http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. http://purl.obolibrary.org/obo/MS_1002300 amaZon Speed ETD http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray. http://purl.obolibrary.org/obo/MS_1002301 amaZon Speed http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. http://purl.obolibrary.org/obo/MS_1002302 Bruker Container format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Bruker Container raw file format. http://purl.obolibrary.org/obo/MS_1002303 Bruker Container nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native identifier (UUID). http://purl.obolibrary.org/obo/MS_1002305 value between 0 and 1 inclusive http://purl.obolibrary.org/obo/MS_1002304 domain range Value range for probabilities. http://purl.obolibrary.org/obo/MS_1002306 value greater than zero http://purl.obolibrary.org/obo/MS_1002304 domain range Positive value range. http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type http://purl.obolibrary.org/obo/MS_1001221 product ion attribute Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion. http://purl.obolibrary.org/obo/MS_1002308 fluorescence detector http://purl.obolibrary.org/obo/MS_1000026 detector type A detector using a fluorescent signal after excitation with light. http://purl.obolibrary.org/obo/MS_1002309 Byonic: Peptide AbsLogProb http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM. http://purl.obolibrary.org/obo/MS_1002310 Byonic: Protein AbsLogProb http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein. http://purl.obolibrary.org/obo/MS_1002311 Byonic: Peptide AbsLogProb2D http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information. http://purl.obolibrary.org/obo/MS_1002312 MS-Numpress linear prediction compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression using MS-Numpress linear prediction compression. http://purl.obolibrary.org/obo/MS_1002313 MS-Numpress positive integer compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression using MS-Numpress positive integer compression. http://purl.obolibrary.org/obo/MS_1002314 MS-Numpress short logged float compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression using MS-Numpress short logged float compression. http://purl.obolibrary.org/obo/MS_1002315 consensus result http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Indicates a consensus result from several search engine runs. http://purl.obolibrary.org/obo/MS_1002316 ProteomeDiscoverer:Amanda:high confidence threshold http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Strict confidence probability score. http://purl.obolibrary.org/obo/MS_1002317 ProteomeDiscoverer:Amanda:middle confidence threshold http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Relaxed confidence probability score. http://purl.obolibrary.org/obo/MS_1002318 ProteomeDiscoverer:automatic workload http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Flag indicating automatic estimation of the workload level. http://purl.obolibrary.org/obo/MS_1002319 Amanda:AmandaScore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Amanda score of the scoring function for a PSM. http://purl.obolibrary.org/obo/MS_1002320 ProteomeDiscoverer:max differential modifications http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum dynamic modifications per PSM. http://purl.obolibrary.org/obo/MS_1002321 ProteomeDiscoverer:max equal modifications http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum equal modifications per PSM. http://purl.obolibrary.org/obo/MS_1002322 ProteomeDiscoverer:min peptide length http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Minimum peptide length. http://purl.obolibrary.org/obo/MS_1002323 ProteomeDiscoverer:max peptide length http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum peptide length. http://purl.obolibrary.org/obo/MS_1002324 ProteomeDiscoverer:max number neutral loss http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Maximum number of same neutral losses. http://purl.obolibrary.org/obo/MS_1002325 ProteomeDiscoverer:max number neutral loss modifications http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Max number of same neutral losses of modifications. http://purl.obolibrary.org/obo/MS_1002326 ProteomeDiscoverer:use flanking ions http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Flag for usage of flanking ions. http://purl.obolibrary.org/obo/MS_1002327 ProteomeDiscoverer:max number of same modifs http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter The maximum number of possible equal modifications per PSM. http://purl.obolibrary.org/obo/MS_1002328 ProteomeDiscoverer:perform deisotoping http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Defines whether a simple deisotoping shall be performed. http://purl.obolibrary.org/obo/MS_1002329 ProteomeDiscoverer:ion settings http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the fragment ions and neutral losses that are calculated. http://purl.obolibrary.org/obo/MS_1002330 ProteomeDiscoverer:3. Static Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter. http://purl.obolibrary.org/obo/MS_1002331 ProteomeDiscoverer:5. Dynamic Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter. http://purl.obolibrary.org/obo/MS_1002332 lab head http://purl.obolibrary.org/obo/MS_1002033 contact role The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group. http://purl.obolibrary.org/obo/MS_1002333 conversion software http://purl.obolibrary.org/obo/MS_1001457 data processing software Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process. http://purl.obolibrary.org/obo/MS_1002334 ProCon http://purl.obolibrary.org/obo/MS_1002333 conversion software Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML. http://purl.obolibrary.org/obo/MS_1002335 PRIDE Converter2 http://purl.obolibrary.org/obo/MS_1002333 conversion software Java software designed to convert one of several proteomics identification results formats into PRIDE XML. http://purl.obolibrary.org/obo/MS_1002336 Amanda http://purl.obolibrary.org/obo/MS_1001456 analysis software Amanda scoring system for PSM identification. http://purl.obolibrary.org/obo/MS_1002337 Andromeda http://purl.obolibrary.org/obo/MS_1001456 analysis software Andromeda is a peptide search engine. http://purl.obolibrary.org/obo/MS_1002338 Andromeda:score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The probability based score of the Andromeda search engine. http://purl.obolibrary.org/obo/MS_1002339 site:global FDR http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Estimation of global false discovery rate of peptides with a post-translational modification. http://purl.obolibrary.org/obo/MS_1002340 ProteomeXchange project tag http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project. http://purl.obolibrary.org/obo/MS_1002341 second-pass peptide identification http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search. http://purl.obolibrary.org/obo/MS_1002342 mzmine http://purl.obolibrary.org/obo/MS_1001457 data processing software A framework for differential analysis of mass spectrometry data. http://purl.obolibrary.org/obo/MS_1002344 Maltcms http://purl.obolibrary.org/obo/MS_1001457 data processing software Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers. http://purl.obolibrary.org/obo/MS_1002345 PSM-level attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Attribute of a single peptide-spectrum match. http://purl.obolibrary.org/obo/MS_1002346 protein group-level identification attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Protein group level information. http://purl.obolibrary.org/obo/MS_1002347 PSM-level identification statistic http://purl.obolibrary.org/obo/MS_1002345 PSM-level attribute Identification confidence metric for a peptide spectrum match. http://purl.obolibrary.org/obo/MS_1002348 protein group-level identification statistic http://purl.obolibrary.org/obo/MS_1002346 protein group-level identification attribute Identification confidence metric for a protein group. http://purl.obolibrary.org/obo/MS_1002349 value greater than zero but less than or equal to one http://purl.obolibrary.org/obo/MS_1002304 domain range Positive value range less than or equal to 1. http://purl.obolibrary.org/obo/MS_1002350 PSM-level global FDR http://purl.obolibrary.org/obo/MS_1002701 PSM-level result list statistic Estimation of the global false discovery rate of peptide spectrum matches. http://purl.obolibrary.org/obo/MS_1002351 PSM-level local FDR http://purl.obolibrary.org/obo/MS_1002347 PSM-level identification statistic Estimation of the local false discovery rate of peptide spectrum matches. http://purl.obolibrary.org/obo/MS_1002352 PSM-level p-value http://purl.obolibrary.org/obo/MS_1002347 PSM-level identification statistic Estimation of the p-value for peptide spectrum matches. http://purl.obolibrary.org/obo/MS_1002353 PSM-level e-value http://purl.obolibrary.org/obo/MS_1002347 PSM-level identification statistic Estimation of the e-value for peptide spectrum matches. http://purl.obolibrary.org/obo/MS_1002354 PSM-level q-value http://purl.obolibrary.org/obo/MS_1002347 PSM-level identification statistic Estimation of the q-value for peptide spectrum matches. http://purl.obolibrary.org/obo/MS_1002355 PSM-level FDRScore http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins mzidLibrary FDRScore for peptide spectrum matches. http://purl.obolibrary.org/obo/MS_1002356 PSM-level combined FDRScore http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. http://purl.obolibrary.org/obo/MS_1002357 PSM-level probability http://purl.obolibrary.org/obo/MS_1002347 PSM-level identification statistic Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum. http://purl.obolibrary.org/obo/MS_1002358 search engine specific peptide sequence-level identification statistic http://purl.obolibrary.org/obo/MS_1001092 peptide sequence-level identification statistic Search engine specific distinct peptide score. http://purl.obolibrary.org/obo/MS_1002359 peptide sequence-level local FDR http://purl.obolibrary.org/obo/MS_1001092 peptide sequence-level identification statistic Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). http://purl.obolibrary.org/obo/MS_1002360 distinct peptide-level FDRScore http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). http://purl.obolibrary.org/obo/MS_1002361 distinct peptide-level combined FDRScore http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools. http://purl.obolibrary.org/obo/MS_1002362 peptide sequence-level probability http://purl.obolibrary.org/obo/MS_1001092 peptide sequence-level identification statistic Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs. http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Search engine specific protein scores. http://purl.obolibrary.org/obo/MS_1002364 protein-level local FDR http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Estimation of the local false discovery rate of proteins. http://purl.obolibrary.org/obo/MS_1002365 FDRScore for proteins http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. http://purl.obolibrary.org/obo/MS_1002366 combined FDRScore for proteins http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins MzidLibrary Combined FDRScore for proteins. http://purl.obolibrary.org/obo/MS_1002367 probability for proteins http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups http://purl.obolibrary.org/obo/MS_1002348 protein group-level identification statistic Search engine specific protein group scores. http://purl.obolibrary.org/obo/MS_1002369 protein group-level global FDR http://purl.obolibrary.org/obo/MS_1002706 protein group-level result list statistic Estimation of the global false discovery rate of protein groups. http://purl.obolibrary.org/obo/MS_1002370 protein group-level local FDR http://purl.obolibrary.org/obo/MS_1002348 protein group-level identification statistic Estimation of the local false discovery rate of protein groups. http://purl.obolibrary.org/obo/MS_1002371 protein group-level p-value http://purl.obolibrary.org/obo/MS_1002348 protein group-level identification statistic Estimation of the p-value for protein groups. http://purl.obolibrary.org/obo/MS_1002372 protein group-level e-value http://purl.obolibrary.org/obo/MS_1002348 protein group-level identification statistic Estimation of the e-value for protein groups. http://purl.obolibrary.org/obo/MS_1002373 protein group-level q-value http://purl.obolibrary.org/obo/MS_1002348 protein group-level identification statistic Estimation of the q-value for protein groups. http://purl.obolibrary.org/obo/MS_1002374 protein group-level FDRScore http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups mzidLibrary FDRScore for protein groups. http://purl.obolibrary.org/obo/MS_1002375 protein group-level combined FDRScore http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. http://purl.obolibrary.org/obo/MS_1002376 protein group-level probability http://purl.obolibrary.org/obo/MS_1002348 protein group-level identification statistic Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. http://purl.obolibrary.org/obo/MS_1002377 ProteomeDiscoverer:Relaxed Score Threshold http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the threshold value for relaxed scoring. http://purl.obolibrary.org/obo/MS_1002378 ProteomeDiscoverer:Strict Score Threshold http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Specifies the threshold value for strict scoring. http://purl.obolibrary.org/obo/MS_1002379 ProteomeDiscoverer:Peptide Without Protein Cut Off Score http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Cut off score for storing peptides that do not belong to a protein. http://purl.obolibrary.org/obo/MS_1002380 false localization rate http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Estimation of the false localization rate for modification site assignment. http://purl.obolibrary.org/obo/MS_1002381 MALDI Solutions LC-MALDI http://purl.obolibrary.org/obo/MS_1001557 Shimadzu Corporation software Software for automated LC-MALDI analysis and reporting. http://purl.obolibrary.org/obo/MS_1002382 Shimadzu MALDI-7090 http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Shimadzu MALDI-7090: MALDI-TOF-TOF. http://purl.obolibrary.org/obo/MS_1002383 SCiLS software http://purl.obolibrary.org/obo/MS_1000531 software SCiLS software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1002384 SCiLS Lab http://purl.obolibrary.org/obo/MS_1002383 SCiLS software SCiLS Lab software. http://purl.obolibrary.org/obo/MS_1002385 SCiLS Lab format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format SCiLS Lab file format. http://purl.obolibrary.org/obo/MS_1002386 preprocessing software http://purl.obolibrary.org/obo/MS_1001457 data processing software Preprocessing software. http://purl.obolibrary.org/obo/MS_1002387 PIA http://purl.obolibrary.org/obo/MS_1002414 postprocessing software PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis. http://purl.obolibrary.org/obo/MS_1002388 PIA XML format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format A compilation of search engine results in the PIA XML format. http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter http://purl.obolibrary.org/obo/MS_1002105 software specific input parameter A parameter set for a single PIA analysis. http://purl.obolibrary.org/obo/MS_1002390 PIA:FDRScore calculated http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter Indicates whether the FDR score was calculated for the input file. http://purl.obolibrary.org/obo/MS_1002391 PIA:Combined FDRScore calculated http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter Indicates whether the combined FDR score was calculated for the PIA compilation. http://purl.obolibrary.org/obo/MS_1002392 PIA:PSM sets created http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter Indicates whether PSM sets were created. http://purl.obolibrary.org/obo/MS_1002393 PIA:used top identifications for FDR http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter The number of top identifications per spectrum used for the FDR calculation, 0 means all. http://purl.obolibrary.org/obo/MS_1002394 PIA:protein score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The score given to a protein by any protein inference. http://purl.obolibrary.org/obo/MS_1002395 PIA:protein inference http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter The used algorithm for the protein inference using PIA. http://purl.obolibrary.org/obo/MS_1002396 PIA:protein inference filter http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter A filter used by PIA for the protein inference. http://purl.obolibrary.org/obo/MS_1002397 PIA:protein inference scoring http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter The used scoring method for the protein inference using PIA. http://purl.obolibrary.org/obo/MS_1002398 PIA:protein inference used score http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter The used base score for the protein inference using PIA. http://purl.obolibrary.org/obo/MS_1002399 PIA:protein inference used PSMs http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter The method to determine the PSMs used for scoring by the protein inference. http://purl.obolibrary.org/obo/MS_1002400 PIA:filter http://purl.obolibrary.org/obo/MS_1002389 PIA workflow parameter A filter used for the report generation. http://purl.obolibrary.org/obo/MS_1002401 leading protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members. http://purl.obolibrary.org/obo/MS_1002402 non-leading protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence. http://purl.obolibrary.org/obo/MS_1002403 group representative http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative. http://purl.obolibrary.org/obo/MS_1002404 count of identified proteins http://purl.obolibrary.org/obo/MS_4000003 single value The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file. http://purl.obolibrary.org/obo/MS_1002405 protein group-level result list attribute http://purl.obolibrary.org/obo/MS_1002699 result list attribute Details describing a protein cluster. http://purl.obolibrary.org/obo/MS_1002406 count of identified clusters http://purl.obolibrary.org/obo/MS_1002405 protein group-level result list attribute The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. http://purl.obolibrary.org/obo/MS_1002407 cluster identifier http://purl.obolibrary.org/obo/MS_1002698 protein cluster identification attribute An identifier applied to protein groups to indicate that they are linked by shared peptides. http://purl.obolibrary.org/obo/MS_1002408 number of distinct protein sequences http://purl.obolibrary.org/obo/MS_1002405 protein group-level result list attribute The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. http://purl.obolibrary.org/obo/MS_1002409 marginally distinguished protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group. http://purl.obolibrary.org/obo/MS_1002410 Anubis http://purl.obolibrary.org/obo/MS_1001139 quantitation software name Anubis software for selected reaction monitoring data. http://purl.obolibrary.org/obo/MS_1002411 TraML format http://purl.obolibrary.org/obo/MS_1002128 method file format The TraML format for transitions in SRM from the PSI. File extension '.TraML'. http://purl.obolibrary.org/obo/MS_1002412 total XIC area http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM). http://purl.obolibrary.org/obo/MS_1002413 product background http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The background area for the quantified transition. http://purl.obolibrary.org/obo/MS_1002414 postprocessing software http://purl.obolibrary.org/obo/MS_1001457 data processing software Postprocessing software. http://purl.obolibrary.org/obo/MS_1002415 protein group passes threshold http://purl.obolibrary.org/obo/MS_1002346 protein group-level identification attribute A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file. http://purl.obolibrary.org/obo/MS_1002416 Orbitrap Fusion http://purl.obolibrary.org/obo/MS_1003770 quadrupole ion trap orbitrap instrument Thermo Scientific Orbitrap Fusion. http://purl.obolibrary.org/obo/MS_1002417 Orbitrap Fusion ETD http://purl.obolibrary.org/obo/MS_1003770 quadrupole ion trap orbitrap instrument Thermo Scientific Orbitrap Fusion with ETD. http://purl.obolibrary.org/obo/MS_1002418 TSQ Quantiva http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ Quantiva MS. http://purl.obolibrary.org/obo/MS_1002419 TSQ Endura http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ Endura MS. http://purl.obolibrary.org/obo/MS_1002420 PASSEL experiment URI http://purl.obolibrary.org/obo/MS_1000878 external reference identifier URI that allows access to a PASSEL experiment. http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to Paragon. http://purl.obolibrary.org/obo/MS_1002422 Paragon: sample type http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation. http://purl.obolibrary.org/obo/MS_1002423 Paragon: cysteine alkylation http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation. http://purl.obolibrary.org/obo/MS_1002424 Paragon: instrument setting http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument. http://purl.obolibrary.org/obo/MS_1002425 Paragon: search effort http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search. http://purl.obolibrary.org/obo/MS_1002426 Paragon: ID focus http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions. http://purl.obolibrary.org/obo/MS_1002427 Paragon: FDR analysis http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting that controls whether FDR analysis is conducted. http://purl.obolibrary.org/obo/MS_1002428 Paragon: quantitation http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting that controls whether quantitation analysis is conducted. http://purl.obolibrary.org/obo/MS_1002429 Paragon: background correction http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples. http://purl.obolibrary.org/obo/MS_1002430 Paragon: bias correction http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity. http://purl.obolibrary.org/obo/MS_1002431 Paragon: channel to use as denominator in ratios http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios. http://purl.obolibrary.org/obo/MS_1002432 search engine specific input metadata http://purl.obolibrary.org/obo/MS_1001249 search input details Search engine specific metadata that are not user-controlled settings. http://purl.obolibrary.org/obo/MS_1002433 Paragon: modified data dictionary or parameter translation http://purl.obolibrary.org/obo/MS_1002432 search engine specific input metadata This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result. http://purl.obolibrary.org/obo/MS_1002434 number of spectra searched http://purl.obolibrary.org/obo/MS_1001249 search input details Number of spectra in a search. http://purl.obolibrary.org/obo/MS_1002435 data processing start time http://purl.obolibrary.org/obo/MS_1000630 data processing parameter The time that a data processing action was started. http://purl.obolibrary.org/obo/MS_1002436 Paragon: digestion http://purl.obolibrary.org/obo/MS_1001249 search input details The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done. http://purl.obolibrary.org/obo/MS_1002437 number of decoy sequences http://purl.obolibrary.org/obo/MS_1001011 search database details The number of decoy sequences, if the concatenated target-decoy approach is used. http://purl.obolibrary.org/obo/MS_1002439 final PSM list http://purl.obolibrary.org/obo/MS_1002438 spectrum identification list result details A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult. http://purl.obolibrary.org/obo/MS_1002440 intermediate PSM list http://purl.obolibrary.org/obo/MS_1002438 spectrum identification list result details A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult. http://purl.obolibrary.org/obo/MS_1002441 Andi-MS format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format AIA Analytical Data Interchange file format for mass spectrometry data. http://purl.obolibrary.org/obo/MS_1002442 chromatograph file format http://purl.obolibrary.org/obo/MS_1001459 file format The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. http://purl.obolibrary.org/obo/MS_1002443 Andi-CHROM format http://purl.obolibrary.org/obo/MS_1002442 chromatograph file format AIA Analytical Data Interchange file format for chromatography data. http://purl.obolibrary.org/obo/MS_1002444 6420 Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002445 6460 Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity. http://purl.obolibrary.org/obo/MS_1002446 6490 Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity. http://purl.obolibrary.org/obo/MS_1002447 Paragon:special factor http://purl.obolibrary.org/obo/MS_1002421 Paragon input parameter The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects. http://purl.obolibrary.org/obo/MS_1002448 PEAKS:inChorusPeptideScore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The PEAKS inChorus peptide score. http://purl.obolibrary.org/obo/MS_1002449 PEAKS:inChorusProteinScore http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The PEAKS inChorus protein score. http://purl.obolibrary.org/obo/MS_1002450 param: b ion-H3PO4 DEPRECATED http://purl.obolibrary.org/obo/MS_1001066 ions series considered in search Ion b-H3PO4: b ion with lost phosphoric acid. http://purl.obolibrary.org/obo/MS_1002451 param: y ion-H3PO4 DEPRECATED http://purl.obolibrary.org/obo/MS_1001066 ions series considered in search Ion y-H3PO4: y ion with lost phosphoric acid. http://purl.obolibrary.org/obo/MS_1002452 Maui http://purl.obolibrary.org/obo/MS_1001457 data processing software The Maltcms Graphical User Interface. http://purl.obolibrary.org/obo/MS_1002453 No fixed modifications searched http://purl.obolibrary.org/obo/MS_1002094 common search engine input parameter No fixed modifications are included as a parameter for the search, and therefore they are not reported. http://purl.obolibrary.org/obo/MS_1002454 No variable modifications searched http://purl.obolibrary.org/obo/MS_1002094 common search engine input parameter No variable modifications are included as a parameter for the search, and therefore they are not reported. http://purl.obolibrary.org/obo/MS_1002455 H2O neutral loss http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search OBSOLETE Neutral loss of water. http://purl.obolibrary.org/obo/MS_1002456 NH3 neutral loss http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search OBSOLETE Neutral loss of ammonia. http://purl.obolibrary.org/obo/MS_1002457 H3PO4 neutral loss http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search OBSOLETE Neutral loss of phosphoric acid. http://purl.obolibrary.org/obo/MS_1002458 PeptideShaker http://purl.obolibrary.org/obo/MS_1001456 analysis software PeptideShaker is a software for the interpretation of proteomics identification results. http://purl.obolibrary.org/obo/MS_1002459 MS Amanda csv format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format MS Amanda csv output format. http://purl.obolibrary.org/obo/MS_1002460 protein group-level global FNR http://purl.obolibrary.org/obo/MS_1002706 protein group-level result list statistic Estimation of the global false negative rate of protein groups. http://purl.obolibrary.org/obo/MS_1002461 protein group-level confidence http://purl.obolibrary.org/obo/MS_1002348 protein group-level identification statistic Estimation of the global confidence of protein groups. http://purl.obolibrary.org/obo/MS_1002462 peptide sequence-level global FNR http://purl.obolibrary.org/obo/MS_1002703 peptide sequence-level result list statistic Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). http://purl.obolibrary.org/obo/MS_1002463 peptide sequence-level global confidence http://purl.obolibrary.org/obo/MS_1002703 peptide sequence-level result list statistic Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). http://purl.obolibrary.org/obo/MS_1002464 PSM-level global FNR http://purl.obolibrary.org/obo/MS_1002701 PSM-level result list statistic Estimation of the global false negative rate of peptide spectrum matches. http://purl.obolibrary.org/obo/MS_1002465 PSM-level global confidence http://purl.obolibrary.org/obo/MS_1002701 PSM-level result list statistic Estimation of the global confidence of peptide spectrum matches. http://purl.obolibrary.org/obo/MS_1002466 PeptideShaker PSM score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The probability based PeptideShaker PSM score. http://purl.obolibrary.org/obo/MS_1002467 PeptideShaker PSM confidence http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The probability based PeptideShaker PSM confidence. http://purl.obolibrary.org/obo/MS_1002468 PeptideShaker peptide score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The probability based PeptideShaker peptide score. http://purl.obolibrary.org/obo/MS_1002469 PeptideShaker peptide confidence http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The probability based PeptideShaker peptide confidence. http://purl.obolibrary.org/obo/MS_1002470 PeptideShaker protein group score http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups The probability based PeptideShaker protein group score. http://purl.obolibrary.org/obo/MS_1002471 PeptideShaker protein group confidence http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The probability based PeptideShaker protein group confidence. http://purl.obolibrary.org/obo/MS_1002472 trap-type collision-induced dissociation http://purl.obolibrary.org/obo/MS_1000133 collision-induced dissociation A collision-induced dissociation process that occurs in a trap-type collision cell. http://purl.obolibrary.org/obo/MS_1002473 ion series considered in search http://purl.obolibrary.org/obo/MS_1001249 search input details The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine. http://purl.obolibrary.org/obo/MS_1002474 ProteoAnnotator:non-canonical gene model score http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group. http://purl.obolibrary.org/obo/MS_1002475 ProteoAnnotator:count alternative peptides http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups The count of the number of peptide sequences mapped to non-canonical gene models only within the group. http://purl.obolibrary.org/obo/MS_1002476 ion mobility drift time http://purl.obolibrary.org/obo/MS_1003254 peak attribute Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated. http://purl.obolibrary.org/obo/MS_1002477 mean ion mobility drift time array http://purl.obolibrary.org/obo/MS_1002893 ion mobility array Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. http://purl.obolibrary.org/obo/MS_1002478 mean charge array http://purl.obolibrary.org/obo/MS_1000513 binary data array Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum. http://purl.obolibrary.org/obo/MS_1002480 regular expression for a digital object identifier (DOI) http://purl.obolibrary.org/obo/MS_1002479 regular expression (10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?!["&'<>])[^ \r \v\f])+). http://purl.obolibrary.org/obo/MS_1002481 higher energy beam-type collision-induced dissociation http://purl.obolibrary.org/obo/MS_1000422 beam-type collision-induced dissociation A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV. http://purl.obolibrary.org/obo/MS_1002482 statistical threshold http://purl.obolibrary.org/obo/MS_1001060 quality estimation method details Estimated statistical threshold. http://purl.obolibrary.org/obo/MS_1002483 PSM-level statistical threshold http://purl.obolibrary.org/obo/MS_1002573 spectrum identification statistical threshold Estimated statistical threshold at PSM-level. http://purl.obolibrary.org/obo/MS_1002484 peptide-level statistical threshold http://purl.obolibrary.org/obo/MS_1002573 spectrum identification statistical threshold Estimated statistical threshold at peptide-level. http://purl.obolibrary.org/obo/MS_1002485 protein-level statistical threshold http://purl.obolibrary.org/obo/MS_1002572 protein detection statistical threshold Estimated statistical threshold at protein-level. http://purl.obolibrary.org/obo/MS_1002486 protein group-level statistical threshold http://purl.obolibrary.org/obo/MS_1002572 protein detection statistical threshold Estimated statistical threshold at protein group-level. http://purl.obolibrary.org/obo/MS_1002487 MassIVE dataset identifier http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. http://purl.obolibrary.org/obo/MS_1002488 MassIVE dataset URI http://purl.obolibrary.org/obo/MS_1000878 external reference identifier URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. http://purl.obolibrary.org/obo/MS_1002489 special processing http://purl.obolibrary.org/obo/MS_1001080 search type Details describing a special processing. http://purl.obolibrary.org/obo/MS_1002490 peptide-level scoring http://purl.obolibrary.org/obo/MS_1002489 special processing Peptide-level scoring performed. http://purl.obolibrary.org/obo/MS_1002491 modification localization scoring http://purl.obolibrary.org/obo/MS_1002489 special processing Modification localization scoring performed. http://purl.obolibrary.org/obo/MS_1002492 consensus scoring http://purl.obolibrary.org/obo/MS_1002489 special processing Consensus multiple search engine approach performed. http://purl.obolibrary.org/obo/MS_1002493 sample pre-fractionation http://purl.obolibrary.org/obo/MS_1002489 special processing Sample pre-fractionation performed. http://purl.obolibrary.org/obo/MS_1002494 crosslinking search http://purl.obolibrary.org/obo/MS_1002489 special processing Crosslinking search performed. http://purl.obolibrary.org/obo/MS_1002495 no special processing http://purl.obolibrary.org/obo/MS_1002489 special processing No special processing performed. http://purl.obolibrary.org/obo/MS_1002496 group PSMs by sequence http://purl.obolibrary.org/obo/MS_1002658 identification parameter Group PSMs by distinct peptide sequence ignoring modifications. http://purl.obolibrary.org/obo/MS_1002497 group PSMs by sequence with modifications http://purl.obolibrary.org/obo/MS_1002658 identification parameter Group PSMs by distinct peptide sequence with taking modifications into account. http://purl.obolibrary.org/obo/MS_1002498 group PSMs by sequence with modifications and charge http://purl.obolibrary.org/obo/MS_1002658 identification parameter Group PSMs by distinct peptide sequence with taking modifications and charge into account. http://purl.obolibrary.org/obo/MS_1002499 peptide level score http://purl.obolibrary.org/obo/MS_1002358 search engine specific peptide sequence-level identification statistic OBSOLETE Peptide level score. http://purl.obolibrary.org/obo/MS_1002500 peptide passes threshold http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file. http://purl.obolibrary.org/obo/MS_1002501 no PSM threshold http://purl.obolibrary.org/obo/MS_1002701 PSM-level result list statistic Indicating that no PSM threshold was used. http://purl.obolibrary.org/obo/MS_1002502 no peptide-level threshold http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute Indicating that no peptide-level threshold was used. http://purl.obolibrary.org/obo/MS_1002503 PSM is used for peptide-level scoring http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute Flags a PSM that it is used for peptide-level scoring. http://purl.obolibrary.org/obo/MS_1002504 modification index http://purl.obolibrary.org/obo/MS_1001055 modification parameters The order of modifications to be referenced elsewhere in the document. http://purl.obolibrary.org/obo/MS_1002505 regular expression for modification localization scoring http://purl.obolibrary.org/obo/MS_1002479 regular expression (?[0-9]+):(?[01][.][0-9]+(?:[Ee][+-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false) http://purl.obolibrary.org/obo/MS_1002506 modification position score http://purl.obolibrary.org/obo/MS_1001055 modification parameters Modification position score. http://purl.obolibrary.org/obo/MS_1002507 modification rescoring:false localization rate http://purl.obolibrary.org/obo/MS_1002506 modification position score Mod position score: false localization rate. http://purl.obolibrary.org/obo/MS_1002508 crosslinking attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Crosslinking attribute. http://purl.obolibrary.org/obo/MS_1002509 crosslink donor http://purl.obolibrary.org/obo/MS_1002508 crosslinking attribute The crosslinking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. http://purl.obolibrary.org/obo/MS_1002510 crosslink acceptor http://purl.obolibrary.org/obo/MS_1002508 crosslinking attribute Crosslinking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. http://purl.obolibrary.org/obo/MS_1002511 crosslink spectrum identification item http://purl.obolibrary.org/obo/MS_1002508 crosslinking attribute Crosslinked spectrum identification item. http://purl.obolibrary.org/obo/MS_1002512 crosslinking score http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins Crosslinking scoring value. http://purl.obolibrary.org/obo/MS_1002513 molecules per cell http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The absolute abundance of protein in a cell. http://purl.obolibrary.org/obo/MS_1002514 absolute quantitation analysis http://purl.obolibrary.org/obo/MS_1001833 quantitation analysis summary Absolute quantitation analysis. http://purl.obolibrary.org/obo/MS_1002515 internal peptide reference used http://purl.obolibrary.org/obo/MS_1001832 quantitation software comment or customizations States whether an internal peptide reference is used or not in absolute quantitation analysis. http://purl.obolibrary.org/obo/MS_1002516 internal protein reference used http://purl.obolibrary.org/obo/MS_1001832 quantitation software comment or customizations States whether an internal protein reference is used or not in absolute quantitation analysis. http://purl.obolibrary.org/obo/MS_1002517 internal reference abundance http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis. http://purl.obolibrary.org/obo/MS_1002518 Progenesis:protein group normalised abundance http://purl.obolibrary.org/obo/MS_1002739 protein group-level quantification datatype The data type normalised abundance for protein groups produced by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1002519 Progenesis:protein group raw abundance http://purl.obolibrary.org/obo/MS_1002739 protein group-level quantification datatype The data type raw abundance for protein groups produced by Progenesis LC-MS. http://purl.obolibrary.org/obo/MS_1002520 peptide group ID http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute Peptide group identifier for peptide-level stats. http://purl.obolibrary.org/obo/MS_1002521 mass spectrometry imaging http://purl.obolibrary.org/obo/MS_1000857 run attribute A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position. http://purl.obolibrary.org/obo/MS_1002522 ProteomeDiscoverer:1. Static Terminal Modification http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Determine 1st static terminal post-translational modifications (PTMs). http://purl.obolibrary.org/obo/MS_1002523 Q Exactive HF http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Q Exactive. http://purl.obolibrary.org/obo/MS_1002524 PepFinder http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific PepFinder BioPharma analysis software. http://purl.obolibrary.org/obo/MS_1002525 TSQ 8000 Evo http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ 8000 Evo MS. http://purl.obolibrary.org/obo/MS_1002526 Exactive Plus http://purl.obolibrary.org/obo/MS_1003953 orbitrap instrument Thermo Scientific Exactive Plus MS. http://purl.obolibrary.org/obo/MS_1002527 instrument specific scan attribute http://purl.obolibrary.org/obo/MS_1000503 scan attribute Instrument specific scan properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1002528 synchronous prefilter selection http://purl.obolibrary.org/obo/MS_1002527 instrument specific scan attribute Synchronous prefilter selection. http://purl.obolibrary.org/obo/MS_1002529 resolution array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of resolution values. http://purl.obolibrary.org/obo/MS_1002530 baseline array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of signal baseline values (the signal in the absence of analytes). http://purl.obolibrary.org/obo/MS_1002531 UIMF format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data. http://purl.obolibrary.org/obo/MS_1002532 UIMF nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1002533 TripleTOF 6600 http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002534 ProLuCID:xcorr http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The ProLuCID result 'XCorr'. http://purl.obolibrary.org/obo/MS_1002535 ProLuCID:deltacn http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The ProLuCID result 'DeltaCn'. http://purl.obolibrary.org/obo/MS_1002536 D-Score http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic D-Score for PTM site location at the PSM-level. http://purl.obolibrary.org/obo/MS_1002537 MD-Score http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic MD-Score for PTM site location at the PSM-level. http://purl.obolibrary.org/obo/MS_1002538 PTM localization confidence metric http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Localization confidence metric for a post translational modification (PTM). http://purl.obolibrary.org/obo/MS_1002539 PeptideShaker PTM confidence type http://purl.obolibrary.org/obo/MS_1002538 PTM localization confidence metric PeptideShaker quality criteria for the confidence of PTM localizations. http://purl.obolibrary.org/obo/MS_1002540 PeptideShaker PSM confidence type http://purl.obolibrary.org/obo/MS_1002347 PSM-level identification statistic PeptideShaker quality criteria for the confidence of PSM's. http://purl.obolibrary.org/obo/MS_1002541 PeptideShaker peptide confidence type http://purl.obolibrary.org/obo/MS_1002358 search engine specific peptide sequence-level identification statistic PeptideShaker quality criteria for the confidence of peptide identifications. http://purl.obolibrary.org/obo/MS_1002542 PeptideShaker protein confidence type http://purl.obolibrary.org/obo/MS_1001116 single protein identification statistic PeptideShaker quality criteria for the confidence of protein identifications. http://purl.obolibrary.org/obo/MS_1002543 xiFDR http://purl.obolibrary.org/obo/MS_1001456 analysis software Target/Decoy based FDR estimation for crosslinking peptide-identifications. http://purl.obolibrary.org/obo/MS_1002544 xi http://purl.obolibrary.org/obo/MS_1001456 analysis software Search engine for crosslinked peptides. http://purl.obolibrary.org/obo/MS_1002545 xi:score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The xi result 'Score'. http://purl.obolibrary.org/obo/MS_1002546 Skyline mzQuantML converter http://purl.obolibrary.org/obo/MS_1001456 analysis software A software package to convert Skyline report to mzQuantML. http://purl.obolibrary.org/obo/MS_1002547 normalized spectral abundance factor http://purl.obolibrary.org/obo/MS_1001805 quantification datatype A normalized spectral abundance factor (NSAF). http://purl.obolibrary.org/obo/MS_1002548 distributed normalized spectral abundance factor http://purl.obolibrary.org/obo/MS_1001805 quantification datatype A distributed normalized spectral abundance factor (dNSAF). http://purl.obolibrary.org/obo/MS_1002549 PTM localization distinct peptide-level statistic http://purl.obolibrary.org/obo/MS_1002689 PTM localization single result statistic Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence. http://purl.obolibrary.org/obo/MS_1002550 peptide:phosphoRS score http://purl.obolibrary.org/obo/MS_1002549 PTM localization distinct peptide-level statistic phosphoRS score for PTM site location at the peptide-level. http://purl.obolibrary.org/obo/MS_1002551 peptide:Ascore http://purl.obolibrary.org/obo/MS_1002549 PTM localization distinct peptide-level statistic A-score for PTM site location at the peptide-level. http://purl.obolibrary.org/obo/MS_1002552 peptide:H-Score http://purl.obolibrary.org/obo/MS_1002549 PTM localization distinct peptide-level statistic H-Score for peptide phosphorylation site location at the peptide-level. http://purl.obolibrary.org/obo/MS_1002553 peptide:D-Score http://purl.obolibrary.org/obo/MS_1002549 PTM localization distinct peptide-level statistic D-Score for PTM site location at the peptide-level. http://purl.obolibrary.org/obo/MS_1002554 peptide:MD-Score http://purl.obolibrary.org/obo/MS_1002549 PTM localization distinct peptide-level statistic MD-Score for PTM site location at the peptide-level. http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Threshold for PTM site location score. http://purl.obolibrary.org/obo/MS_1002556 Ascore threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for Ascore PTM site location score. http://purl.obolibrary.org/obo/MS_1002557 D-Score threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for D-score PTM site location score. http://purl.obolibrary.org/obo/MS_1002558 MD-Score threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for MD-score PTM site location score. http://purl.obolibrary.org/obo/MS_1002559 H-Score threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for H-score PTM site location score. http://purl.obolibrary.org/obo/MS_1002560 DeBunker:score threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for DeBunker PTM site location score. http://purl.obolibrary.org/obo/MS_1002561 Mascot:PTM site assignment confidence threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for Mascot PTM site assignment confidence. http://purl.obolibrary.org/obo/MS_1002562 MSQuant:PTM-score threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for MSQuant:PTM-score. http://purl.obolibrary.org/obo/MS_1002563 MaxQuant:PTM Score threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for MaxQuant:PTM Score. http://purl.obolibrary.org/obo/MS_1002564 MaxQuant:P-site localization probability threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for MaxQuant:P-site localization probability. http://purl.obolibrary.org/obo/MS_1002565 MaxQuant:PTM Delta Score threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for MaxQuant:PTM Delta Score. http://purl.obolibrary.org/obo/MS_1002566 MaxQuant:Phospho (STY) Probabilities threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for MaxQuant:Phospho (STY) Probabilities. http://purl.obolibrary.org/obo/MS_1002567 phosphoRS score threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for phosphoRS score. http://purl.obolibrary.org/obo/MS_1002568 phosphoRS site probability threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold Threshold for phosphoRS site probability. http://purl.obolibrary.org/obo/MS_1002569 ProteomeDiscoverer:Number of Spectra Processed At Once http://purl.obolibrary.org/obo/MS_1002101 ProteomeDiscoverer input parameter Number of spectra processed at once in a ProteomeDiscoverer search. http://purl.obolibrary.org/obo/MS_1002570 sequence multiply subsumable protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group. http://purl.obolibrary.org/obo/MS_1002571 spectrum multiply subsumable protein http://purl.obolibrary.org/obo/MS_1001101 protein group or subset relationship A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group. http://purl.obolibrary.org/obo/MS_1002572 protein detection statistical threshold http://purl.obolibrary.org/obo/MS_1002482 statistical threshold Estimated statistical threshold used for protein detection. http://purl.obolibrary.org/obo/MS_1002573 spectrum identification statistical threshold http://purl.obolibrary.org/obo/MS_1002482 statistical threshold Estimated statistical threshold used for spectrum identification. http://purl.obolibrary.org/obo/MS_1002574 ASAPRatio http://purl.obolibrary.org/obo/MS_1002286 Trans-Proteomic Pipeline software A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. http://purl.obolibrary.org/obo/MS_1002575 Tide http://purl.obolibrary.org/obo/MS_1001456 analysis software Tide open-source sequence search program developed at the University of Washington. http://purl.obolibrary.org/obo/MS_1002576 Andromeda result format http://purl.obolibrary.org/obo/MS_1001040 intermediate analysis format Andromeda result file output format. http://purl.obolibrary.org/obo/MS_1002577 2000 QTRAP http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument SCIEX 2000 QTRAP. http://purl.obolibrary.org/obo/MS_1002578 2500 QTRAP http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument SCIEX 2500 QTRAP. http://purl.obolibrary.org/obo/MS_1002579 3500 QTRAP http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument SCIEX 3500 QTRAP. http://purl.obolibrary.org/obo/MS_1002580 QTRAP 4500 http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument SCIEX QTRAP 4500. http://purl.obolibrary.org/obo/MS_1002581 QTRAP 6500 http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument SCIEX QTRAP 6500. http://purl.obolibrary.org/obo/MS_1002582 QTRAP 6500+ http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument SCIEX QTRAP 6500+. http://purl.obolibrary.org/obo/MS_1002583 TripleTOF 4600 http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX TripleTOF 4600 time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002584 TripleTOF 5600+ http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX TripleTOF 5600+ time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002585 API 100 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Applied Biosystems/MDS SCIEX API 100 MS. http://purl.obolibrary.org/obo/MS_1002586 API 100LC http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Applied Biosystems/MDS SCIEX API 100LC MS. http://purl.obolibrary.org/obo/MS_1002587 API 165 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Applied Biosystems/MDS SCIEX API 165 MS. http://purl.obolibrary.org/obo/MS_1002588 API 300 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Applied Biosystems/MDS SCIEX API 300 MS. http://purl.obolibrary.org/obo/MS_1002589 API 350 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Applied Biosystems/MDS SCIEX API 350 MS. http://purl.obolibrary.org/obo/MS_1002590 API 365 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Applied Biosystems/MDS SCIEX API 365 MS. http://purl.obolibrary.org/obo/MS_1002591 Triple Quad 3500 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX Triple Quad 3500. http://purl.obolibrary.org/obo/MS_1002592 Triple Quad 4500 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX Triple Quad 4500. http://purl.obolibrary.org/obo/MS_1002593 Triple Quad 5500 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX Triple Quad 5500. http://purl.obolibrary.org/obo/MS_1002594 Triple Quad 6500 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX Triple Quad 6500. http://purl.obolibrary.org/obo/MS_1002595 Triple Quad 6500+ http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX Triple Quad 6500+. http://purl.obolibrary.org/obo/MS_1002596 ProLuCID http://purl.obolibrary.org/obo/MS_1001456 analysis software The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute. http://purl.obolibrary.org/obo/MS_1002597 MS1 format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format MS1 file format for MS1 spectral data. http://purl.obolibrary.org/obo/MS_1002598 DTASelect http://purl.obolibrary.org/obo/MS_1001456 analysis software Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches. http://purl.obolibrary.org/obo/MS_1002599 splash key http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Spectral Hash key, an unique identifier for spectra. http://purl.obolibrary.org/obo/MS_1002600 PRIDE XML http://purl.obolibrary.org/obo/MS_1002130 identification file format Internal data and submission format of the PRIDE database. http://purl.obolibrary.org/obo/MS_1002601 mzTab http://purl.obolibrary.org/obo/MS_1000914 tab delimited text format Tabular result format for proteomics and metabolomics experiments. http://purl.obolibrary.org/obo/MS_1002602 sample label http://purl.obolibrary.org/obo/MS_1002111 assay label attribute Reagent used in labeled quantification methods. http://purl.obolibrary.org/obo/MS_1002603 ICAT reagent http://purl.obolibrary.org/obo/MS_1002602 sample label Isotope coded affinity tag reagent. http://purl.obolibrary.org/obo/MS_1002604 ICAT heavy reagent http://purl.obolibrary.org/obo/MS_1002603 ICAT reagent The name of the sample labelled with the heavy ICAT label. http://purl.obolibrary.org/obo/MS_1002605 ICAT light reagent http://purl.obolibrary.org/obo/MS_1002603 ICAT reagent The name of the sample labelled with the light ICAT label. http://purl.obolibrary.org/obo/MS_1002606 ICPL reagent http://purl.obolibrary.org/obo/MS_1002602 sample label Isotope coded protein labeling reagent. http://purl.obolibrary.org/obo/MS_1002607 ICPL reagent 0 http://purl.obolibrary.org/obo/MS_1002606 ICPL reagent The name of the sample labelled with the ICPL reagent 0. http://purl.obolibrary.org/obo/MS_1002608 ICPL reagent 4 http://purl.obolibrary.org/obo/MS_1002606 ICPL reagent The name of the sample labelled with the ICPL reagent 4. http://purl.obolibrary.org/obo/MS_1002609 ICPL reagent 6 http://purl.obolibrary.org/obo/MS_1002606 ICPL reagent The name of the sample labelled with the ICPL reagent 6. http://purl.obolibrary.org/obo/MS_1002610 ICPL reagent 10 http://purl.obolibrary.org/obo/MS_1002606 ICPL reagent The name of the sample labelled with the ICPL reagent 10. http://purl.obolibrary.org/obo/MS_1002611 SILAC reagent http://purl.obolibrary.org/obo/MS_1002602 sample label Stable isotope labeling with amino acids in cell culture reagent. http://purl.obolibrary.org/obo/MS_1002612 SILAC heavy reagent http://purl.obolibrary.org/obo/MS_1002611 SILAC reagent The name of the sample labelled with the heavy SILAC label. http://purl.obolibrary.org/obo/MS_1002613 SILAC medium reagent http://purl.obolibrary.org/obo/MS_1002611 SILAC reagent The name of the sample labelled with the medium SILAC label. http://purl.obolibrary.org/obo/MS_1002614 SILAC light reagent http://purl.obolibrary.org/obo/MS_1002611 SILAC reagent The name of the sample labelled with the light SILAC label. http://purl.obolibrary.org/obo/MS_1002615 TMT reagent http://purl.obolibrary.org/obo/MS_1002602 sample label Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling. http://purl.obolibrary.org/obo/MS_1002616 TMT reagent 126 http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 126. http://purl.obolibrary.org/obo/MS_1002617 TMT reagent 127 http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 127. http://purl.obolibrary.org/obo/MS_1002618 TMT reagent 128 http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 128. http://purl.obolibrary.org/obo/MS_1002619 TMT reagent 129 http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 129. http://purl.obolibrary.org/obo/MS_1002620 TMT reagent 130 http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 130. http://purl.obolibrary.org/obo/MS_1002621 TMT reagent 131 http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 131. http://purl.obolibrary.org/obo/MS_1002622 iTRAQ reagent http://purl.obolibrary.org/obo/MS_1002602 sample label Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent. http://purl.obolibrary.org/obo/MS_1002623 iTRAQ reagent 113 http://purl.obolibrary.org/obo/MS_1002622 iTRAQ reagent The name of the sample labelled with the iTRAQ reagent 113. http://purl.obolibrary.org/obo/MS_1002624 iTRAQ reagent 114 http://purl.obolibrary.org/obo/MS_1002622 iTRAQ reagent The name of the sample labelled with the iTRAQ reagent 114. http://purl.obolibrary.org/obo/MS_1002625 iTRAQ reagent 115 http://purl.obolibrary.org/obo/MS_1002622 iTRAQ reagent The name of the sample labelled with the iTRAQ reagent 115. http://purl.obolibrary.org/obo/MS_1002626 iTRAQ reagent 116 http://purl.obolibrary.org/obo/MS_1002622 iTRAQ reagent The name of the sample labelled with the iTRAQ reagent 116. http://purl.obolibrary.org/obo/MS_1002627 iTRAQ reagent 117 http://purl.obolibrary.org/obo/MS_1002622 iTRAQ reagent The name of the sample labelled with the iTRAQ reagent 117. http://purl.obolibrary.org/obo/MS_1002628 iTRAQ reagent 118 http://purl.obolibrary.org/obo/MS_1002622 iTRAQ reagent The name of the sample labelled with the iTRAQ reagent 118. http://purl.obolibrary.org/obo/MS_1002629 iTRAQ reagent 119 http://purl.obolibrary.org/obo/MS_1002622 iTRAQ reagent The name of the sample labelled with the iTRAQ reagent 119. http://purl.obolibrary.org/obo/MS_1002630 iTRAQ reagent 121 http://purl.obolibrary.org/obo/MS_1002622 iTRAQ reagent The name of the sample labelled with the iTRAQ reagent 121. http://purl.obolibrary.org/obo/MS_1002631 electron-transfer/higher-energy collision dissociation http://purl.obolibrary.org/obo/MS_1003181 combined dissociation method Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy). http://purl.obolibrary.org/obo/MS_1002632 jPOST dataset identifier http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. http://purl.obolibrary.org/obo/MS_1002633 jPOST dataset URI http://purl.obolibrary.org/obo/MS_1000878 external reference identifier URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. http://purl.obolibrary.org/obo/MS_1002634 Q Exactive Plus http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Q Exactive Plus. http://purl.obolibrary.org/obo/MS_1002635 proteogenomics search http://purl.obolibrary.org/obo/MS_1002489 special processing Proteogenomics search performed. http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute Proteogenomics attribute. http://purl.obolibrary.org/obo/MS_1002637 chromosome name http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute The name or number of the chromosome to which a given peptide has been mapped. http://purl.obolibrary.org/obo/MS_1002638 chromosome strand http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute The strand (+ or -) to which the peptide has been mapped. http://purl.obolibrary.org/obo/MS_1002639 peptide start on chromosome http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system. http://purl.obolibrary.org/obo/MS_1002640 peptide end on chromosome http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system. http://purl.obolibrary.org/obo/MS_1002641 peptide exon count http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute The number of exons to which the peptide has been mapped. http://purl.obolibrary.org/obo/MS_1002642 peptide exon nucleotide sizes http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length. http://purl.obolibrary.org/obo/MS_1002643 peptide start positions on chromosome http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome. http://purl.obolibrary.org/obo/MS_1002644 genome reference version http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference. http://purl.obolibrary.org/obo/MS_1002645 MSDK http://purl.obolibrary.org/obo/MS_1001457 data processing software Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data. http://purl.obolibrary.org/obo/MS_1002647 Thermo nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Thermo comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002648 Waters nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Waters comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002649 WIFF nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra WIFF comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002650 Bruker/Agilent YEP nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002651 Bruker BAF nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002652 Bruker FID nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002653 multiple peak list nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002654 single peak list nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002655 scan number only nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002656 spectrum identifier nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002657 mzML unique identifier, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002659 UniProtKB text sequence format http://purl.obolibrary.org/obo/MS_1001347 database file formats Text-based format used by UniProtKB for sequence entries. http://purl.obolibrary.org/obo/MS_1002660 UniProtKB XML sequence format http://purl.obolibrary.org/obo/MS_1001347 database file formats XML-based format used by UniProtKB for sequence entries. http://purl.obolibrary.org/obo/MS_1002661 Morpheus http://purl.obolibrary.org/obo/MS_1001456 analysis software Morpheus search engine. http://purl.obolibrary.org/obo/MS_1002662 Morpheus:Morpheus score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Morpheus score for PSMs. http://purl.obolibrary.org/obo/MS_1002663 Morpheus:summed Morpheus score http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups Summed Morpheus score for protein groups. http://purl.obolibrary.org/obo/MS_1002664 interaction score derived from crosslinking http://purl.obolibrary.org/obo/MS_1002675 crosslinking result details Parent term for interaction scores derived from crosslinking. http://purl.obolibrary.org/obo/MS_1002665 regular expression for interaction scores derived from crosslinking http://purl.obolibrary.org/obo/MS_1002479 regular expression ((?[0-9]+)[.](?[a|b]):(?[0-9]+|null):(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?):(?true|false))|(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?) http://purl.obolibrary.org/obo/MS_1002666 impact II http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' impact II. http://purl.obolibrary.org/obo/MS_1002667 impact HD http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' impact HD. http://purl.obolibrary.org/obo/MS_1002668 frag: iTRAQ 4plex reporter ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114. http://purl.obolibrary.org/obo/MS_1002669 frag: iTRAQ 8plex reporter ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113. http://purl.obolibrary.org/obo/MS_1002670 frag: TMT reporter ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N. http://purl.obolibrary.org/obo/MS_1002671 frag: TMT ETD reporter ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C. http://purl.obolibrary.org/obo/MS_1002672 no modification threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold No statistical threshold for accepting or rejecting that a modification position. http://purl.obolibrary.org/obo/MS_1002673 OpenXQuest http://purl.obolibrary.org/obo/MS_1000752 TOPP software Cross-Linking MS search engine. http://purl.obolibrary.org/obo/MS_1002674 X500R QTOF http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002676 protein-pair-level global FDR http://purl.obolibrary.org/obo/MS_1002664 interaction score derived from crosslinking Estimation of the global false discovery rate of proteins-pairs in crosslinking experiments. http://purl.obolibrary.org/obo/MS_1002677 residue-pair-level global FDR http://purl.obolibrary.org/obo/MS_1002664 interaction score derived from crosslinking Estimation of the global false discovery rate of residue-pairs in crosslinking experiments. http://purl.obolibrary.org/obo/MS_1002678 supplemental beam-type collision-induced dissociation http://purl.obolibrary.org/obo/MS_1000422 beam-type collision-induced dissociation A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation. http://purl.obolibrary.org/obo/MS_1002679 supplemental collision-induced dissociation http://purl.obolibrary.org/obo/MS_1000133 collision-induced dissociation The dissociation of an ion after supplemental collisional excitation. http://purl.obolibrary.org/obo/MS_1002680 supplemental collision energy http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion. http://purl.obolibrary.org/obo/MS_1002681 OpenXQuest:combined score http://purl.obolibrary.org/obo/MS_1001153 search engine specific score OpenXQuest's combined score for a crosslink spectrum match. http://purl.obolibrary.org/obo/MS_1002682 OpenXQuest:xcorr xlink http://purl.obolibrary.org/obo/MS_1001153 search engine specific score OpenXQuest's cross-correlation of crosslinked ions subscore. http://purl.obolibrary.org/obo/MS_1002683 OpenXQuest:xcorr common http://purl.obolibrary.org/obo/MS_1001153 search engine specific score OpenXQuest's cross-correlation of unlinked ions subscore. http://purl.obolibrary.org/obo/MS_1002684 OpenXQuest:match-odds http://purl.obolibrary.org/obo/MS_1001153 search engine specific score OpenXQuest's match-odds subscore. http://purl.obolibrary.org/obo/MS_1002685 OpenXQuest:intsum http://purl.obolibrary.org/obo/MS_1001153 search engine specific score OpenXQuest's sum of matched peak intensity subscore. http://purl.obolibrary.org/obo/MS_1002686 OpenXQuest:wTIC http://purl.obolibrary.org/obo/MS_1001153 search engine specific score OpenXQuest's weighted percent of total ion current subscore. http://purl.obolibrary.org/obo/MS_1002687 analysis attribute http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Attribute of an item in the result of mass spectrometry proteomics data analysis. http://purl.obolibrary.org/obo/MS_1002688 PTM localization attribute http://purl.obolibrary.org/obo/MS_1002687 analysis attribute Statistic derived from a post-translational modification localization analysis. http://purl.obolibrary.org/obo/MS_1002689 PTM localization single result statistic http://purl.obolibrary.org/obo/MS_1002688 PTM localization attribute Statistic for a single item derived from a post-translational modification localization analysis. http://purl.obolibrary.org/obo/MS_1002690 PTM localization result list statistic http://purl.obolibrary.org/obo/MS_1002688 PTM localization attribute Statistic for all items derived from a post-translational modification localization analysis. http://purl.obolibrary.org/obo/MS_1002691 global FLR http://purl.obolibrary.org/obo/MS_1002690 PTM localization result list statistic Global false localization rate for all localizations in a dataset. http://purl.obolibrary.org/obo/MS_1002692 local FLR at threshold http://purl.obolibrary.org/obo/MS_1002690 PTM localization result list statistic Local false localization rate for the bottom item in list of localizations sorted from most to least confident. http://purl.obolibrary.org/obo/MS_1002693 identification attribute http://purl.obolibrary.org/obo/MS_1002687 analysis attribute Attribute of an identification item in the result of mass spectrometry proteomics data analysis. http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute http://purl.obolibrary.org/obo/MS_1002693 identification attribute Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis. http://purl.obolibrary.org/obo/MS_1002695 frag: isobaric label ion http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragment ion corresponding to an isobaric label artifact. http://purl.obolibrary.org/obo/MS_1002697 secondary isotope peak http://purl.obolibrary.org/obo/MS_1002307 fragmentation ion type Fragment ion that is an isotopic peak other than the monoisotopic peak. This is used in conjunction with another ion type, such as frag: y ion. http://purl.obolibrary.org/obo/MS_1002698 protein cluster identification attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute An attribute of the protein cluster concept as used in mzIdentML. http://purl.obolibrary.org/obo/MS_1002699 result list attribute http://purl.obolibrary.org/obo/MS_1002693 identification attribute General property of an entire result list. http://purl.obolibrary.org/obo/MS_1002700 PSM-level result list attribute http://purl.obolibrary.org/obo/MS_1002699 result list attribute General property of the list of all PSMs. http://purl.obolibrary.org/obo/MS_1002701 PSM-level result list statistic http://purl.obolibrary.org/obo/MS_1002700 PSM-level result list attribute Statistic pertaining to the full list of all PSMs. http://purl.obolibrary.org/obo/MS_1002702 peptide sequence-level result list attribute http://purl.obolibrary.org/obo/MS_1002699 result list attribute General property of all peptide sequences in the list. http://purl.obolibrary.org/obo/MS_1002703 peptide sequence-level result list statistic http://purl.obolibrary.org/obo/MS_1002702 peptide sequence-level result list attribute Statistic pertaining to all peptide sequences in the list. http://purl.obolibrary.org/obo/MS_1002704 protein-level result list attribute http://purl.obolibrary.org/obo/MS_1002699 result list attribute Attribute of an entire protein list. http://purl.obolibrary.org/obo/MS_1002705 protein-level result list statistic http://purl.obolibrary.org/obo/MS_1002704 protein-level result list attribute A statistical metric of an entire protein list. http://purl.obolibrary.org/obo/MS_1002706 protein group-level result list statistic http://purl.obolibrary.org/obo/MS_1002405 protein group-level result list attribute Attribute of an entire list of protein groups. http://purl.obolibrary.org/obo/MS_1002719 Pegasus BT http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO bench-top GC time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002720 MSPathFinder http://purl.obolibrary.org/obo/MS_1001456 analysis software PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra. http://purl.obolibrary.org/obo/MS_1002721 MSPathFinder:SpecEValue http://purl.obolibrary.org/obo/MS_1002353 PSM-level e-value MSPathFinder spectral E-value. http://purl.obolibrary.org/obo/MS_1002722 MSPathFinder:EValue http://purl.obolibrary.org/obo/MS_1002353 PSM-level e-value MSPathFinder E-value. http://purl.obolibrary.org/obo/MS_1002723 MSPathFinder:QValue http://purl.obolibrary.org/obo/MS_1002354 PSM-level q-value MSPathFinder Q-value. http://purl.obolibrary.org/obo/MS_1002724 MSPathFinder:PepQValue http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic MSPathFinder peptide-level Q-value. http://purl.obolibrary.org/obo/MS_1002725 MSPathFinder:RawScore http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic MSPathFinder raw score. http://purl.obolibrary.org/obo/MS_1002726 SYNAPT G2-Si http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002727 MALDI SYNAPT G2-Si http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002728 Vion IMS QTof http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002729 Xevo G2-XS Tof http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002730 Xevo TQ-XS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002731 Xevo TQ-S micro http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002732 Orbitrap Fusion Lumos http://purl.obolibrary.org/obo/MS_1003770 quadrupole ion trap orbitrap instrument Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. http://purl.obolibrary.org/obo/MS_1002733 peptide-level spectral count http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting. http://purl.obolibrary.org/obo/MS_1002734 peptide ion-level spectral count http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting. http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type of the value reported in a QuantLayer for a feature. http://purl.obolibrary.org/obo/MS_1002736 PSM-level quantification datatype http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type of the value reported in a QuantLayer for a PSM. http://purl.obolibrary.org/obo/MS_1002737 peptide-level quantification datatype http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type of the value reported in a QuantLayer for a peptide. http://purl.obolibrary.org/obo/MS_1002738 protein-level quantification datatype http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type of the value reported in a QuantLayer for a protein. http://purl.obolibrary.org/obo/MS_1002739 protein group-level quantification datatype http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type of the value reported in a QuantLayer for a protein group. http://purl.obolibrary.org/obo/MS_1002740 unmapped peptide http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location. http://purl.obolibrary.org/obo/MS_1002741 unmapped protein http://purl.obolibrary.org/obo/MS_1002636 proteogenomics attribute Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location. http://purl.obolibrary.org/obo/UO_0000110 pascal http://purl.obolibrary.org/obo/UO_0000109 pressure unit A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]. http://purl.obolibrary.org/obo/UO_0000111 energy unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc). http://purl.obolibrary.org/obo/UO_0000112 joule http://purl.obolibrary.org/obo/UO_0000111 energy unit An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force. http://purl.obolibrary.org/obo/UO_0000166 parts per notation unit http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance. http://purl.obolibrary.org/obo/UO_0000169 parts per million http://purl.obolibrary.org/obo/UO_0000166 parts per notation unit A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]. http://purl.obolibrary.org/obo/UO_0000221 dalton http://purl.obolibrary.org/obo/UO_0000002 mass unit An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state. http://purl.obolibrary.org/obo/UO_0000222 kilodalton http://purl.obolibrary.org/obo/UO_0000002 mass unit A mass unit which is equal to one thousand daltons. http://purl.obolibrary.org/obo/UO_0000227 magnetic flux density unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the strength of a magnetic field. http://purl.obolibrary.org/obo/UO_0000228 tesla http://purl.obolibrary.org/obo/UO_0000227 magnetic flux density unit A magnetic flux density unit which is equal to one weber per square meter. http://purl.obolibrary.org/obo/UO_0000266 electronvolt http://purl.obolibrary.org/obo/UO_0000111 energy unit A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J. http://purl.obolibrary.org/obo/UO_0000267 electric field strength unit http://purl.obolibrary.org/obo/UO_0000000 unit The electric field strength is a unit which is a measure of the potential difference between two points some distance apart. http://purl.obolibrary.org/obo/UO_0000268 volt per meter http://purl.obolibrary.org/obo/UO_0000267 electric field strength unit The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart. http://purl.obolibrary.org/obo/UO_0000269 absorbance unit http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light. http://purl.obolibrary.org/obo/UO_0000324 square angstrom http://purl.obolibrary.org/obo/UO_0000047 area unit An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long. http://purl.obolibrary.org/obo/MS_1002874 TSQ Altis http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ Altis Triple Quadrupole MS. http://purl.obolibrary.org/obo/MS_1002875 TSQ Quantis http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ Quantis Triple Quadrupole MS. http://purl.obolibrary.org/obo/MS_1002876 TSQ 9000 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ 9000 Triple Quadrupole MS. http://purl.obolibrary.org/obo/MS_1002877 Q Exactive HF-X http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS. http://purl.obolibrary.org/obo/MS_1003021 Fixed modification http://purl.obolibrary.org/obo/MS_1003026 named element in mzIdentML Post-translational modification which is assumed to be present at each instance of a residue type. http://purl.obolibrary.org/obo/MS_1003022 Variable modification http://purl.obolibrary.org/obo/MS_1003026 named element in mzIdentML Post-translational modification which may or may not be present at a residue type. http://purl.obolibrary.org/obo/MS_1003032 compound identification confidence code in MS-DIAL http://purl.obolibrary.org/obo/MS_1002895 small molecule identification attribute The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program. http://purl.obolibrary.org/obo/MS_1001327 Spectronaut http://purl.obolibrary.org/obo/MS_1003207 library creation software Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data. http://purl.obolibrary.org/obo/MS_1002714 FLASHDeconv http://purl.obolibrary.org/obo/MS_1001457 data processing software Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. http://purl.obolibrary.org/obo/MS_1003291 Luciphor deltaScore http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic Luciphor phosphosite localization score http://purl.obolibrary.org/obo/MS_1003292 TSQ Altis Plus http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ Altis Plus Triple Quadrupole MS. http://purl.obolibrary.org/obo/MS_1003293 ZenoTOF 7600 http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX ZenoTOF 7600. http://purl.obolibrary.org/obo/MS_1003294 electron activated dissociation http://purl.obolibrary.org/obo/MS_1000250 electron capture dissociation A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. http://purl.obolibrary.org/obo/MS_1003295 summary statistics of replicates http://purl.obolibrary.org/obo/MS_1003064 spectrum aggregation attribute Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum. http://purl.obolibrary.org/obo/MS_1003296 number of replicates spectra used from source http://purl.obolibrary.org/obo/MS_1003064 spectrum aggregation attribute The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name' http://purl.obolibrary.org/obo/MS_1003297 contributing replicate spectrum http://purl.obolibrary.org/obo/MS_1003257 library spectrum cross reference A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum. http://purl.obolibrary.org/obo/MS_1003301 peptide-spectrum match http://purl.obolibrary.org/obo/MS_1003300 spectrum match Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence. http://purl.obolibrary.org/obo/MS_1003302 spectrum-spectrum match http://purl.obolibrary.org/obo/MS_1003300 spectrum match Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering. http://purl.obolibrary.org/obo/MS_1003303 spectral similarity http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone. http://purl.obolibrary.org/obo/MS_1003304 spectral dot product http://purl.obolibrary.org/obo/MS_1003303 spectral similarity The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity. http://purl.obolibrary.org/obo/MS_1003305 spectral Euclidean distance http://purl.obolibrary.org/obo/MS_1003303 spectral similarity The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space. http://purl.obolibrary.org/obo/MS_1003306 shared peak count http://purl.obolibrary.org/obo/MS_1003303 spectral similarity The number of peaks with closely matching m/z values that are common to two spectra. http://purl.obolibrary.org/obo/MS_1003307 normalized spectral angle http://purl.obolibrary.org/obo/MS_1003303 spectral similarity The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi. http://purl.obolibrary.org/obo/MS_1003308 spectral Pearson correlation http://purl.obolibrary.org/obo/MS_1003303 spectral similarity The Pearson's rho statistic between a pair of points representing two vectorized spectra. http://purl.obolibrary.org/obo/MS_1003309 Goslin http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software The Goslin implementations parse common lipid name dialects and normalize them to the recent lipid shorthand nomenclature based on grammars on succinct lipid nomenclature. http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level http://purl.obolibrary.org/obo/MS_1002895 small molecule identification attribute Identification confidence levels based on the updated lipid shorthand nomenclature. The value slot can have the values 'Category', 'Class', 'Species', 'Phosphate-position', 'Molecular species', 'sn-position', 'DBE position', 'Structure defined', 'Full structure', 'Complete structure'. http://purl.obolibrary.org/obo/MS_1003311 Lipid empirical score http://purl.obolibrary.org/obo/MS_1002888 small molecule confidence measure The lipid empirical score is a point-based lipid class-specific scoring system based on MS and other evidence sources as defined by the Lipidomics Standards Initiative (LSI). The score has a numeric value between 0 and 100. Score values are lipid class-specific and are therefore not immediately comparable between lipid classes. http://purl.obolibrary.org/obo/MS_1003312 Lipid shorthand identification confidence - Category http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'Category'. http://purl.obolibrary.org/obo/MS_1003313 Lipid shorthand identification confidence - Class http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'Class'. http://purl.obolibrary.org/obo/MS_1003314 Lipid shorthand identification confidence - Species http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'Species'. http://purl.obolibrary.org/obo/MS_1003315 Lipid shorthand identification confidence - Phosphate-position http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'Phosphate-position'. http://purl.obolibrary.org/obo/MS_1003316 Lipid shorthand identification confidence - Molecular species http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'Molecular species'. http://purl.obolibrary.org/obo/MS_1003317 Lipid shorthand identification confidence - sn-position http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'sn-position'. http://purl.obolibrary.org/obo/MS_1003318 Lipid shorthand identification confidence - DBE pos http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'DBE pos'. http://purl.obolibrary.org/obo/MS_1003319 Lipid shorthand identification confidence - Structure defined http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'Structure defined'. http://purl.obolibrary.org/obo/MS_1003320 spectrum cluster size http://purl.obolibrary.org/obo/MS_1003266 spectrum cluster attribute The number of spectra in a spectrum cluster. http://purl.obolibrary.org/obo/MS_1003321 summary statistics of clustered spectra http://purl.obolibrary.org/obo/MS_1003266 spectrum cluster attribute Summary statistics of an attribute among all spectra of a spectrum cluster. http://purl.obolibrary.org/obo/MS_1003322 spectrum cluster best representative http://purl.obolibrary.org/obo/MS_1003266 spectrum cluster attribute Cross reference to the spectrum that is considered the most representative among spectra in a cluster, either as a library spectrum key if the best representative is in the same library, or a universal spectrum identifier if it is not. http://purl.obolibrary.org/obo/MS_1003323 spectrum cluster consensus spectrum http://purl.obolibrary.org/obo/MS_1003266 spectrum cluster attribute Cross reference to a consensus spectrum that is constructed from aggregating spectra in a cluster, either as a library spectrum key if the consensus spectrum is in the same library, or a universal spectrum identifier if it is not. http://purl.obolibrary.org/obo/MS_1003324 spectral dot product to aggregated spectrum http://purl.obolibrary.org/obo/MS_1003304 spectral dot product Spectral similarity measured by the spectral dot product between a replicate to its corresponding aggregated (e.g. consensus) spectrum. http://purl.obolibrary.org/obo/MS_1003325 Lipid shorthand identification confidence - Full structure http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'Full structure'. http://purl.obolibrary.org/obo/MS_1003326 Lipid shorthand identification confidence - Complete structure http://purl.obolibrary.org/obo/MS_1003310 Lipid shorthand identification confidence level Lipid shorthand identification confidence level 'Complete structure'. http://purl.obolibrary.org/obo/MS_1003327 number of identified protein groups http://purl.obolibrary.org/obo/MS_4000003 single value The number of protein groups that pass the threshold to be considered identified with sufficient confidence. http://purl.obolibrary.org/obo/MS_1003328 number of identified proteoforms http://purl.obolibrary.org/obo/MS_4000003 single value The number of proteoforms that pass the threshold to be considered identified with sufficient confidence. http://purl.obolibrary.org/obo/MS_1003329 looplink spectrum identification item http://purl.obolibrary.org/obo/MS_1002508 crosslinking attribute Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink. http://purl.obolibrary.org/obo/MS_1003330 noncovalently associated peptides search http://purl.obolibrary.org/obo/MS_1002489 special processing Noncovalently associated peptides search performed. Noncovalently associated peptides are two different peptides which were not crosslinked but stayed associated with each other throughout the workflow, due to noncovalent interactions. http://purl.obolibrary.org/obo/MS_1003331 noncovalently associated peptides spectrum identification item http://purl.obolibrary.org/obo/MS_1002508 crosslinking attribute Noncovalently associated peptides spectrum identification item. http://purl.obolibrary.org/obo/MS_1003332 identification based on multiple spectra http://purl.obolibrary.org/obo/MS_1002345 PSM-level attribute Provides an identifier to encode identifications based on multiple spectra. http://purl.obolibrary.org/obo/MS_1003333 regular expression for encoding identifications based on multiple spectra. http://purl.obolibrary.org/obo/MS_1002479 regular expression ^(?[0-9]+)(?::(?P|C))?$ http://purl.obolibrary.org/obo/MS_1003334 parent term for PSM-level scores for identifications based on multiple spectra http://purl.obolibrary.org/obo/MS_1002483 PSM-level statistical threshold Parent term for PSM-level scores for identifications based on multiple spectra. http://purl.obolibrary.org/obo/MS_1003335 regular expression for PSM-level scores for identifications based on multiple spectra http://purl.obolibrary.org/obo/MS_1002479 regular expression ^(?[0-9]+):(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+))$ http://purl.obolibrary.org/obo/MS_1003336 posterior error probability from identification based on multiple spectra http://purl.obolibrary.org/obo/MS_1003334 parent term for PSM-level scores for identifications based on multiple spectra PEP score for identifications based on multiple spectra. http://purl.obolibrary.org/obo/MS_1003337 crosslinked PSM-level global FDR http://purl.obolibrary.org/obo/MS_1002701 PSM-level result list statistic Estimation of the global false discovery rate of crosslinked peptide spectrum matches. http://purl.obolibrary.org/obo/MS_1003338 peptide-pair sequence-level global FDR http://purl.obolibrary.org/obo/MS_1002703 peptide sequence-level result list statistic Estimation of the global false discovery rate for distinct peptide-pairs (id est multiple PSMs have been collapsed to one entry). Applicable in the case of crosslinked peptides or noncovalently associated peptides. http://purl.obolibrary.org/obo/MS_1003339 peptide-pair passes threshold http://purl.obolibrary.org/obo/MS_1001105 peptide sequence-level identification attribute Peptide-pair passes threshold. Applicable in the case of crosslinked peptides or noncovalently associated peptides. http://purl.obolibrary.org/obo/MS_1003340 residue-pair passes threshold http://purl.obolibrary.org/obo/MS_1001060 quality estimation method details Residue-pair passes threshold. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI). http://purl.obolibrary.org/obo/MS_1003341 protein-protein interaction passes threshold http://purl.obolibrary.org/obo/MS_1001060 quality estimation method details Protein-protein interaction passes threshold. http://purl.obolibrary.org/obo/MS_1003342 regular expression for whether interaction score derived from crosslinking passes threshold http://purl.obolibrary.org/obo/MS_1002479 regular expression ^((?[0-9]+):(?true|false))$ http://purl.obolibrary.org/obo/MS_1003343 FDR applied separately to self crosslinks and protein heteromeric crosslinks http://purl.obolibrary.org/obo/MS_1002489 special processing States whether FDR was applied separately to self crosslinks (crosslinks between peptides within one protein sequence) and protein heteromeric crosslinks (crosslinks between distinct protein sequences). http://purl.obolibrary.org/obo/MS_1003344 residue-pair ref http://purl.obolibrary.org/obo/MS_1002508 crosslinking attribute Reference to a residue-pair supported by this identification item, the value is the identifier for the residue-pair. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI). http://purl.obolibrary.org/obo/MS_1003345 regular expression for residue-pair ref http://purl.obolibrary.org/obo/MS_1002479 regular expression ^(([0-9]+).(a|b))$ http://purl.obolibrary.org/obo/MS_1003346 cleavable crosslinker stub http://purl.obolibrary.org/obo/MS_1001471 peptide modification details This term indicates that a given protein modification is a derivative of a cleavable crosslinker. http://purl.obolibrary.org/obo/MS_1003347 Unimod derivative code http://purl.obolibrary.org/obo/MS_1001471 peptide modification details The single letter code in Unimod that identifies a specific derivative of a modification. For example, in UNIMOD:1842 (http://www.unimod.org/modifications_view.php?editid1=1842) the letter ‘W’ represents the derivative ‘water quenched monolink’. http://purl.obolibrary.org/obo/MS_1003349 affinity proteomics http://purl.obolibrary.org/obo/MS_1003348 proteomics large-scale study of proteins and proteomes via the use of affinity reagents. http://purl.obolibrary.org/obo/MS_1003350 mass spectrometry proteomics http://purl.obolibrary.org/obo/MS_1003348 proteomics large-scale study of proteins and proteomes via the use of mass spectrometers to measure the masses and abundances of charged proteins or protein fragments. http://purl.obolibrary.org/obo/MS_1003351 top-down proteomics http://purl.obolibrary.org/obo/MS_1003350 mass spectrometry proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact proteins. http://purl.obolibrary.org/obo/MS_1003352 native top-down proteomics http://purl.obolibrary.org/obo/MS_1003351 top-down proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact folded proteins. http://purl.obolibrary.org/obo/MS_1003353 non-native top-down proteomics http://purl.obolibrary.org/obo/MS_1003351 top-down proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact denatured proteins. http://purl.obolibrary.org/obo/MS_1003354 middle-down proteomics http://purl.obolibrary.org/obo/MS_1003350 mass spectrometry proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of large protein fragments after partial digestion of denatured proteins. http://purl.obolibrary.org/obo/MS_1003355 bottom-up proteomics http://purl.obolibrary.org/obo/MS_1003350 mass spectrometry proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of peptides after complete digestion of denatured proteins. http://purl.obolibrary.org/obo/MS_1003356 Orbitrap Ascend http://purl.obolibrary.org/obo/MS_1003770 quadrupole ion trap orbitrap instrument Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. http://purl.obolibrary.org/obo/MS_1003357 ANN-SoLo http://purl.obolibrary.org/obo/MS_1001456 analysis software ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart. http://purl.obolibrary.org/obo/MS_1003358 XCorr rank http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score. http://purl.obolibrary.org/obo/MS_1003359 exact p-value http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic A p-value for the XCorr score, calculated using dynamic programming. http://purl.obolibrary.org/obo/MS_1003360 refactored XCorr http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum. http://purl.obolibrary.org/obo/MS_1003361 res-ev score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks. http://purl.obolibrary.org/obo/MS_1003362 res-ev rank http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score. http://purl.obolibrary.org/obo/MS_1003363 res-ev p-value http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure. http://purl.obolibrary.org/obo/MS_1003364 combined p-value http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them. http://purl.obolibrary.org/obo/MS_1003365 combined p-value rank http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value. http://purl.obolibrary.org/obo/MS_1003366 tailor score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum. http://purl.obolibrary.org/obo/MS_1003367 monoisotopic mass deisotoping http://purl.obolibrary.org/obo/MS_1000033 deisotoping The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution. http://purl.obolibrary.org/obo/MS_1003368 most abundant mass deisotoping http://purl.obolibrary.org/obo/MS_1000033 deisotoping The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution. http://purl.obolibrary.org/obo/MS_1003370 reduction to summed singly charged peak list http://purl.obolibrary.org/obo/MS_1000543 data processing action The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z. http://purl.obolibrary.org/obo/MS_1003371 SelexION compensation voltage http://purl.obolibrary.org/obo/MS_1003254 peak attribute The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer. http://purl.obolibrary.org/obo/MS_1003373 mzIdentML extension version http://purl.obolibrary.org/obo/MS_1003372 specification document extension version The versioning of an mzIdentML extension document. http://purl.obolibrary.org/obo/MS_1003374 Open Chromatography Binary OCB format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format ChemClipse/OpenChrom file format. http://purl.obolibrary.org/obo/MS_1003375 Conversion to OCB http://purl.obolibrary.org/obo/MS_1000530 file format conversion Conversion of a file format to Open Chromatography Binary OCB file format. http://purl.obolibrary.org/obo/MS_1003376 ChemClipse http://purl.obolibrary.org/obo/MS_1001457 data processing software ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH. http://purl.obolibrary.org/obo/MS_1003377 OpenChrom http://purl.obolibrary.org/obo/MS_1001457 data processing software OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse. http://purl.obolibrary.org/obo/MS_1003378 Orbitrap Astral http://purl.obolibrary.org/obo/MS_1003771 quadrupole orbitrap astral instrument Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer. http://purl.obolibrary.org/obo/MS_1003379 asymmetric track lossless time-of-flight analyzer http://purl.obolibrary.org/obo/MS_1000084 time-of-flight A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution. http://purl.obolibrary.org/obo/MS_1003380 Xevo G3 QTof http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003381 ACQUITY RDa Detector http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Waters Corporation RDa time-of-flight mass detector. http://purl.obolibrary.org/obo/MS_1003382 waters_connect http://purl.obolibrary.org/obo/MS_1001457 data processing software Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing. http://purl.obolibrary.org/obo/MS_1003383 timsTOF Ultra http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker Daltonics' timsTOF Ultra. http://purl.obolibrary.org/obo/MS_1003384 semantic version regexp http://purl.obolibrary.org/obo/MS_1002479 regular expression v?(d+).(d+).(d+)(?:-(S+))? http://purl.obolibrary.org/obo/MS_1003385 mzIdentML crosslinking extension document version http://purl.obolibrary.org/obo/MS_1003373 mzIdentML extension version The versioning of the crosslinking mzIdentML extension document. http://purl.obolibrary.org/obo/MS_1003386 Spectra http://purl.obolibrary.org/obo/MS_1001457 data processing software Bioconductor package Spectra for mass spectrometry data representation and processing. http://purl.obolibrary.org/obo/MS_1003387 MetaboAnnotation http://purl.obolibrary.org/obo/MS_1001457 data processing software Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data. http://purl.obolibrary.org/obo/MS_1003388 CompoundDb http://purl.obolibrary.org/obo/MS_1003207 library creation software Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries. http://purl.obolibrary.org/obo/MS_1003389 mzTab-M http://purl.obolibrary.org/obo/MS_1000914 tab delimited text format Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence. http://purl.obolibrary.org/obo/MS_1003390 crosslinker cleavage characteristics http://purl.obolibrary.org/obo/MS_1001471 peptide modification details Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::. http://purl.obolibrary.org/obo/MS_1003391 crosslinker cleavage regular expression http://purl.obolibrary.org/obo/MS_1002479 regular expression ^(?[A-Za-z]):(?[+-]?[0-9]+(.[0-9]+)?([eE][+-]?[0-9]+(.[0-9]+)?)?):(?[A-Za-z]+)$ http://purl.obolibrary.org/obo/MS_1003392 search modification id http://purl.obolibrary.org/obo/MS_1001471 peptide modification details A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses. http://purl.obolibrary.org/obo/MS_1003393 search modification id ref http://purl.obolibrary.org/obo/MS_1001471 peptide modification details A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance. http://purl.obolibrary.org/obo/MS_1003394 SelexION separation voltage http://purl.obolibrary.org/obo/MS_1003254 peak attribute RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF. http://purl.obolibrary.org/obo/MS_4000095 slowest frequency for MS level 1 collection http://purl.obolibrary.org/obo/MS_4000003 single value The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. http://purl.obolibrary.org/obo/MS_4000096 slowest frequency for MS level 2 collection http://purl.obolibrary.org/obo/MS_4000003 single value The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. http://purl.obolibrary.org/obo/MS_4000097 MS1 signal jump (10x) count http://purl.obolibrary.org/obo/MS_4000003 single value The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. http://purl.obolibrary.org/obo/MS_4000098 MS1 signal fall (10x) count http://purl.obolibrary.org/obo/MS_4000003 single value The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. http://purl.obolibrary.org/obo/MS_4000099 number of empty MS1 scans http://purl.obolibrary.org/obo/MS_4000003 single value Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). http://purl.obolibrary.org/obo/MS_4000100 number of empty MS2 scans http://purl.obolibrary.org/obo/MS_4000003 single value Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). http://purl.obolibrary.org/obo/MS_4000101 number of empty MS3 scans http://purl.obolibrary.org/obo/MS_4000003 single value Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). http://purl.obolibrary.org/obo/MS_4000102 number of detected quantification data points http://purl.obolibrary.org/obo/MS_4000003 single value The number of data points detected for quantification purposes within the run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. http://purl.obolibrary.org/obo/MS_4000103 number of identified quantification data points http://purl.obolibrary.org/obo/MS_4000003 single value The number of identified data points for quantification purposes within the run after user defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000104 total ion currents http://purl.obolibrary.org/obo/MS_4000005 table Tabular representation of the total ion current detected in each of a series of mass spectra. http://purl.obolibrary.org/obo/MS_4000105 ion injection parameters http://purl.obolibrary.org/obo/MS_4000005 table Tabular representation of the parameters around ion selection like the amount of time spent filling an ion trapping device for each scan acquisition. http://purl.obolibrary.org/obo/MS_4000106 MS1 frequency in equal parts of subsequent RT http://purl.obolibrary.org/obo/MS_4000004 n-tuple Average MS1 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.) http://purl.obolibrary.org/obo/MS_4000107 MS2 frequency in equal parts of subsequent RT http://purl.obolibrary.org/obo/MS_4000004 n-tuple Average MS2 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.) http://purl.obolibrary.org/obo/MS_4000108 MS1 peak density distribution mean http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of peak densities in MS1, the mean http://purl.obolibrary.org/obo/MS_4000109 MS1 peak density distribution sigma http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of peak densities in MS1, the sigma value http://purl.obolibrary.org/obo/MS_4000110 MS1 peak density distribution low outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of peak densities in MS1, the list of outliers below a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000111 MS1 peak density distribution high outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of peak densities in MS1, the list of outliers above a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000112 MS2 peak density distribution mean http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of peak densities in MS2, the mean http://purl.obolibrary.org/obo/MS_4000113 MS2 peak density distribution sigma http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of peak densities in MS2, the sigma value http://purl.obolibrary.org/obo/MS_4000114 MS2 peak density distribution low outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of peak densities in MS2, the list of outliers below a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000115 MS2 peak density distribution high outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of peak densities in MS2, the list of outliers above a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000116 MS2 precursor intensity distribution http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. http://purl.obolibrary.org/obo/MS_4000117 MS2 precursor intensity distribution mean http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of MS2 precursor intensities, the mean http://purl.obolibrary.org/obo/MS_4000118 MS2 precursor intensity distribution sigma http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of MS2 precursor intensities, the sigma value http://purl.obolibrary.org/obo/MS_4000119 MS2 precursor intensity distribution low outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of precursor intensities, the list of outliers below a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000120 MS2 precursor intensity distribution high outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of precursor intensities, the list of outliers above a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000121 MS1 signal-to-noise ratio quantiles http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of signal-to-noise ratio in MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 http://purl.obolibrary.org/obo/MS_4000122 MS1 signal-to-noise ratio mean http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of signal-to-noise ratio in MS1, the mean http://purl.obolibrary.org/obo/MS_4000123 MS1 signal-to-noise ratio sigma http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of signal-to-noise ratio in MS1, the sigma value http://purl.obolibrary.org/obo/MS_4000124 MS1 signal-to-noise ratio low outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of signal-to-noise ratio in MS1, the list of outliers below a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000125 MS1 signal-to-noise ratio high outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of signal-to-noise ratio in MS1, the list of outliers above a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000126 MS2 signal-to-noise ratio quantiles http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of signal-to-noise ratio in MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 http://purl.obolibrary.org/obo/MS_4000127 MS2 signal-to-noise ratio mean http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of signal-to-noise ratio in MS2, the mean http://purl.obolibrary.org/obo/MS_4000128 MS2 signal-to-noise ratio sigma http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of signal-to-noise ratio in MS2, the sigma value http://purl.obolibrary.org/obo/MS_4000129 MS2 signal-to-noise ratio low outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of signal-to-noise ratio in MS2, the list of outliers below a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000130 MS2 signal-to-noise ratio high outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of signal-to-noise ratio in MS2, the list of outliers above a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000131 MS1 ion collection time quantiles http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of ion injection times (MS:1000927) for MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 http://purl.obolibrary.org/obo/MS_4000132 MS1 ion collection time mean http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of ion injection times (MS:1000927) for MS1, the mean http://purl.obolibrary.org/obo/MS_4000133 MS1 ion collection time sigma http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of ion injection times (MS:1000927) for MS1, the sigma value http://purl.obolibrary.org/obo/MS_4000134 MS1 ion collection time low outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers below a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000135 MS1 ion collection time high outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers above a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000136 MS2 ion collection time quantiles http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of ion injection times (MS:1000927) for MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 http://purl.obolibrary.org/obo/MS_4000137 MS2 ion collection time mean http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of ion injection times (MS:1000927) for MS2, the mean http://purl.obolibrary.org/obo/MS_4000138 MS2 ion collection time sigma http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of ion injection times (MS:1000927) for MS2, the sigma value http://purl.obolibrary.org/obo/MS_4000139 MS2 ion collection time low outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers below a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000140 MS2 ion collection time high outliers http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers above a in-file defined threshold http://purl.obolibrary.org/obo/MS_4000141 outlier threshold criterion http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term The definition of the outlier criteria applied. http://purl.obolibrary.org/obo/MS_4000142 Tukey's fence http://purl.obolibrary.org/obo/MS_4000141 outlier threshold criterion Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5. http://purl.obolibrary.org/obo/MS_4000143 Tukey's fence high outliers http://purl.obolibrary.org/obo/MS_4000141 outlier threshold criterion Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5. http://purl.obolibrary.org/obo/MS_4000144 Tukey's fence low outliers http://purl.obolibrary.org/obo/MS_4000141 outlier threshold criterion Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5. http://purl.obolibrary.org/obo/MS_4000145 Z-score threshold http://purl.obolibrary.org/obo/MS_4000141 outlier threshold criterion Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. http://purl.obolibrary.org/obo/MS_4000146 Z-score threshold high outliers http://purl.obolibrary.org/obo/MS_4000141 outlier threshold criterion Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. http://purl.obolibrary.org/obo/MS_4000147 Z-score threshold low outliers http://purl.obolibrary.org/obo/MS_4000141 outlier threshold criterion Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. http://purl.obolibrary.org/obo/MS_4000148 algorithmical threshold http://purl.obolibrary.org/obo/MS_4000141 outlier threshold criterion Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used. http://purl.obolibrary.org/obo/MS_4000149 iRT calibration formula http://purl.obolibrary.org/obo/MS_4000004 n-tuple A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc. http://purl.obolibrary.org/obo/MS_4000150 iRT calibration adjusted r-squared http://purl.obolibrary.org/obo/MS_4000003 single value The goodness of fit statistic between observed retention times and iRT calibrated retention times. http://purl.obolibrary.org/obo/MS_4000151 MsQuality http://purl.obolibrary.org/obo/MS_1001456 analysis software MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. http://purl.obolibrary.org/obo/MS_4000152 MS2 precursor median m/z of identified quantification data points http://purl.obolibrary.org/obo/MS_4000003 single value Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000153 interquartile RT period for identified quantification data points http://purl.obolibrary.org/obo/MS_4000003 single value The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000154 rate of the interquartile RT period for identified quantification data points http://purl.obolibrary.org/obo/MS_4000003 single value The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000155 area under TIC http://purl.obolibrary.org/obo/MS_4000003 single value The area under the total ion chromatogram. http://purl.obolibrary.org/obo/MS_4000156 area under TIC RT quantiles http://purl.obolibrary.org/obo/MS_4000004 n-tuple The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple. http://purl.obolibrary.org/obo/MS_4000157 extent of identified MS2 precursor intensity http://purl.obolibrary.org/obo/MS_4000003 single value Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000158 median of TIC values in the RT range in which the middle half of quantification data points are identified http://purl.obolibrary.org/obo/MS_4000003 single value Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000159 median of TIC values in the shortest RT range in which half of the quantification data points are identified http://purl.obolibrary.org/obo/MS_4000003 single value Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000160 MS2 precursor intensity range http://purl.obolibrary.org/obo/MS_4000004 n-tuple Minimum and maximum MS2 precursor intensity recorded. http://purl.obolibrary.org/obo/MS_4000161 identified MS2 precursor intensity distribution http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000162 unidentified MS2 precursor intensity distribution http://purl.obolibrary.org/obo/MS_4000004 n-tuple From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000163 identified MS2 precursor intensity distribution mean http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000164 unidentified MS2 precursor intensity distribution mean http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000165 identified MS2 precursor intensity distribution sigma http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000166 unidentified MS2 precursor intensity distribution sigma http://purl.obolibrary.org/obo/MS_4000003 single value From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000167 ratio of 1+ over 2+ of all MS2 known precursor charges http://purl.obolibrary.org/obo/MS_4000003 single value The ratio of 1+ over 2+ MS2 precursor charge count of all spectra. http://purl.obolibrary.org/obo/MS_4000168 ratio of 1+ over 2+ of identified MS2 known precursor charges http://purl.obolibrary.org/obo/MS_4000003 single value The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000169 ratio of 3+ over 2+ of all MS2 known precursor charges http://purl.obolibrary.org/obo/MS_4000003 single value The ratio of 3+ over 2+ MS2 precursor charge count of all spectra. http://purl.obolibrary.org/obo/MS_4000170 ratio of 3+ over 2+ of identified MS2 known precursor charges http://purl.obolibrary.org/obo/MS_4000003 single value The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000171 ratio of 4+ over 2+ of all MS2 known precursor charges http://purl.obolibrary.org/obo/MS_4000003 single value The ratio of 4+ over 2+ MS2 precursor charge count of all spectra. http://purl.obolibrary.org/obo/MS_4000172 ratio of 4+ over 2+ of identified MS2 known precursor charges http://purl.obolibrary.org/obo/MS_4000003 single value The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000173 mean MS2 precursor charge in all spectra http://purl.obolibrary.org/obo/MS_4000003 single value Mean MS2 precursor charge in all spectra http://purl.obolibrary.org/obo/MS_4000174 mean MS2 precursor charge in identified spectra http://purl.obolibrary.org/obo/MS_4000003 single value Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_4000175 median MS2 precursor charge in all spectra http://purl.obolibrary.org/obo/MS_4000003 single value Median MS2 precursor charge in all spectra http://purl.obolibrary.org/obo/MS_4000176 median MS2 precursor charge in identified spectra http://purl.obolibrary.org/obo/MS_4000003 single value Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_1003408 Scout score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Scout identification search engine score http://purl.obolibrary.org/obo/MS_4000189 DIAMetric http://purl.obolibrary.org/obo/MS_1001456 analysis software DIAMetric is a Data-Independent Acquisition Quality Metric Generator. http://purl.obolibrary.org/obo/MS_1003508 Synapt G1 HDMS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters Synapt G1 HDMS quadrupole - ion mobility - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003526 6410A Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Agilent 6410A Triple Quadrupole LC/MS triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003802 Ionoptika instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Ionoptika Ltd. instrument model. http://purl.obolibrary.org/obo/MS_1003803 Ionoptika software http://purl.obolibrary.org/obo/MS_1000531 software Ionoptika software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1003804 Ionoptika J105 http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Ionoptika J105 time-of-flight secondary ion mass spectrometer. http://purl.obolibrary.org/obo/MS_1003805 J Series III http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Ionoptika J Series III time-of-flight secondary ion mass spectrometer. http://purl.obolibrary.org/obo/MS_1003806 NeoSIMS http://purl.obolibrary.org/obo/MS_1003803 Ionoptika software Ionoptika software for data acquisition. http://purl.obolibrary.org/obo/MS_1003807 Ionoptika Image Analyser http://purl.obolibrary.org/obo/MS_1003803 Ionoptika software Ionoptika software for image data analysis. http://purl.obolibrary.org/obo/MS_1003808 J105 Ionoptika Mass Imager http://purl.obolibrary.org/obo/MS_1003803 Ionoptika software Ionoptika J105 software for mass spectrometry imaging data analysis. http://purl.obolibrary.org/obo/MS_1003809 IoDataConverter http://purl.obolibrary.org/obo/MS_1003803 Ionoptika software Ionoptika software for converting Ionoptika data formats to imzML or HDF5. http://purl.obolibrary.org/obo/MS_1003810 Ionoptika V1 format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Ionoptika data format generated by J105 TOF-SIMS instrument. http://purl.obolibrary.org/obo/MS_1003811 Ionoptika V3 format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Ionoptika data format generated by J105 TOF-SIMS instrument. http://purl.obolibrary.org/obo/NCIT_C25330 Duration http://purl.obolibrary.org/obo/NCIT_C21514 Temporal Qualifier The period of time during which something continues. http://purl.obolibrary.org/obo/NCIT_C41009 Qualifier http://purl.obolibrary.org/obo/NCIT_C20189 Property or Attribute A term that helps define and render a concept unique. http://purl.obolibrary.org/obo/NCIT_C60694 Principal Component http://purl.obolibrary.org/obo/NCIT_C19044 Statistical Technique One of the axes representing the projection of variance resulting from principal component analysis. http://purl.obolibrary.org/obo/MS_1002857 Unsupported dataset by repository http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission. http://purl.obolibrary.org/obo/MS_1002868 Original data http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter One dataset is not a reanalysis of previously published data. http://purl.obolibrary.org/obo/MS_1002859 Additional associated raw file URI http://purl.obolibrary.org/obo/MS_1002845 Associated file URI Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE. http://purl.obolibrary.org/obo/MS_1002854 Peer-reviewed dataset http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter Dataset has been peer-reviewed somehow. http://purl.obolibrary.org/obo/MS_1002872 Panorama Public dataset identifier http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. http://purl.obolibrary.org/obo/MS_1002873 Panorama Public dataset URI http://purl.obolibrary.org/obo/MS_1000878 external reference identifier URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. http://purl.obolibrary.org/obo/MS_1002894 InChIKey http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details Unique chemical structure identifier for chemical compounds. http://purl.obolibrary.org/obo/MS_1002924 TopPIC:combined spectrum number http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Number of combined spectra. http://purl.obolibrary.org/obo/MS_4000181 obsolete identified MS2 quarter RT fraction http://purl.obolibrary.org/obo/MS_4000004 n-tuple OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration. http://purl.obolibrary.org/obo/MS_1003423 Orbitrap Exploris GC 240 http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Orbitrap Exploris GC 240 Mass Spectrometer. http://purl.obolibrary.org/obo/MS_4000025 precursor ion current chromatogram http://purl.obolibrary.org/obo/MS_4000004 n-tuple Representation of the ion current assigned to detected precursors in the series of all MS1 spectra versus time. http://purl.obolibrary.org/obo/MS_4000026 fragment ppm deviation median http://purl.obolibrary.org/obo/MS_4000003 single value The median of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied. http://purl.obolibrary.org/obo/MS_4000027 fragment ppm deviation mean http://purl.obolibrary.org/obo/MS_4000003 single value The mean of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied http://purl.obolibrary.org/obo/MS_4000028 fragment ppm deviation sigma http://purl.obolibrary.org/obo/MS_4000003 single value The standard deviation of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied http://purl.obolibrary.org/obo/MS_4000029 area under TIC in MS1 http://purl.obolibrary.org/obo/MS_4000003 single value The area under the total ion current chromatogram (MS:1000235) of all MS1 spectra. http://purl.obolibrary.org/obo/MS_4000030 area under TIC in MS2 http://purl.obolibrary.org/obo/MS_4000003 single value The area under the total ion current chromatogram (MS:1000235) of all MS2 spectra. http://purl.obolibrary.org/obo/MS_4000031 peak area of MS1 vs MS2 signal ratio http://purl.obolibrary.org/obo/MS_4000003 single value The ratio of the area under TIC of MS1 (MS:4000029) divided by the area under the TIC of MS2 (MS:4000030). http://purl.obolibrary.org/obo/MS_1003448 SCIEX WIFF2 format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format SCIEX WIFF2 file format. http://purl.obolibrary.org/obo/MS_1002993 Q Exactive Focus http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Q Exactive Focus Hybrid Quadrupole-Orbitrap Mass Spectrometer. http://purl.obolibrary.org/obo/MS_1003712 fast gas chromatography http://purl.obolibrary.org/obo/MS_1002272 gas chromatography separation Fast gas chromatography (fast GC, FGC) employs short, narrow-bore capillary columns, high carrier gas velocity, and rapid temperature programming to achieve high-efficiency separations in a fraction of standard GC run times. http://purl.obolibrary.org/obo/MS_1003713 packed column gas chromatography http://purl.obolibrary.org/obo/MS_1002272 gas chromatography separation Packed column gas chromatography uses stainless steel or glass tubes (typically 2–4 mm ID, 1–6 m length) filled with particulate packing material coated with stationary phase, enabling the separation of larger sample volumes but typically providing lower efficiency and broader peaks than capillary GC. http://purl.obolibrary.org/obo/MS_1003714 capillary column gas chromatography http://purl.obolibrary.org/obo/MS_1002272 gas chromatography separation Capillary column gas chromatography uses narrow-bore fused silica columns (typically 0.1–0.5 mm ID, 5–100 m length) coated with a thin internal stationary phase, enabling high-efficiency, high-resolution separations of volatile analytes. http://purl.obolibrary.org/obo/MS_1003715 high-resolution gas chromatography http://purl.obolibrary.org/obo/MS_1002272 gas chromatography separation High-resolution gas chromatography (HRGC) utilizes narrow-bore capillary columns and optimized parameters to achieve exceptional separation efficiency and peak capacity for complex, volatile mixtures. http://purl.obolibrary.org/obo/MS_1003716 pyrolysis-gas chromatography http://purl.obolibrary.org/obo/MS_1002272 gas chromatography separation Pyrolysis-gas chromatography (Py-GC) thermally decomposes complex samples into smaller volatile fragments, which are separated using GC. http://purl.obolibrary.org/obo/MS_1003717 gas-liquid chromatography http://purl.obolibrary.org/obo/MS_1002272 gas chromatography separation Gas-liquid chromatography (GLC) employs an inert gaseous mobile phase and a liquid stationary phase immobilized on a solid support, separating volatile analytes by differential partitioning in the column. http://purl.obolibrary.org/obo/MS_1003718 non-polar stationary phase gas-liquid chromatography http://purl.obolibrary.org/obo/MS_1003717 gas-liquid chromatography Non-polar stationary phase gas-liquid chromatography employs phases like polydimethylsiloxane (PDMS), where separation is based on analyte volatility and dispersion interactions, optimally retaining non-polar compounds. http://purl.obolibrary.org/obo/MS_1003719 mid-polar stationary phase gas-liquid chromatography http://purl.obolibrary.org/obo/MS_1003717 gas-liquid chromatography Mid-polar stationary phase gas-liquid chromatography employs phases such as polysiloxanes, providing balanced separation through both dispersion and dipole interactions for analytes of intermediate polarity. http://purl.obolibrary.org/obo/MS_1003720 polar stationary phase gas-liquid chromatography http://purl.obolibrary.org/obo/MS_1003717 gas-liquid chromatography Polar stationary phase gas-liquid chromatography uses stationary phases such as polyethylene glycol, maximizing retention and selectivity for polar analytes via dipole–dipole and hydrogen bonding interactions. http://purl.obolibrary.org/obo/MS_1003721 chiral stationary phase gas-liquid chromatography http://purl.obolibrary.org/obo/MS_1003717 gas-liquid chromatography Chiral stationary phase gas-liquid chromatography uses a stationary phase with bonded chiral selectors, enabling enantiomeric separation by stereoselective interactions. http://purl.obolibrary.org/obo/MS_1003722 gas-solid chromatography http://purl.obolibrary.org/obo/MS_1002272 gas chromatography separation Gas-solid chromatography (GSC) separates volatile analytes by adsorption onto a solid stationary phase, with elution governed by analyte–surface interactions and adsorption. http://purl.obolibrary.org/obo/MS_1003723 molecular sieve stationary phase gas-solid chromatography http://purl.obolibrary.org/obo/MS_1003722 gas-solid chromatography Molecular sieve stationary phase gas–solid chromatography separates volatile analytes by differential adsorption onto a porous, crystalline aluminosilicate solid phase, enabling selective separation of permanent gases and small hydrocarbons. http://purl.obolibrary.org/obo/MS_1003724 porous polymer stationary phase gas-solid chromatography http://purl.obolibrary.org/obo/MS_1003722 gas-solid chromatography Porous polymer stationary phase gas-solid chromatography employs solid adsorbents like porous polystyrene-divinylbenzene, enabling volatile analyte separation by selective physical adsorption based on molecular size and polarity. http://purl.obolibrary.org/obo/MS_1003725 activated carbon stationary phase gas-solid chromatography http://purl.obolibrary.org/obo/MS_1003722 gas-solid chromatography Activated carbon stationary phase gas-solid chromatography utilizes activated carbon’s high surface area to selectively adsorb and resolve volatile non-polar organics and permanent gases via surface interactions and physical adsorption. http://purl.obolibrary.org/obo/MS_1003726 inorganic oxides stationary phase gas-solid chromatography http://purl.obolibrary.org/obo/MS_1003722 gas-solid chromatography Inorganic oxides stationary phase gas-solid chromatography employs solid adsorbents such as silica or alumina, enabling separation of permanent gases and low-boiling organics by surface adsorption interactions. http://purl.obolibrary.org/obo/MS_1003727 graphitized carbon stationary phase gas-solid chromatography http://purl.obolibrary.org/obo/MS_1003722 gas-solid chromatography Graphitized carbon stationary phase gas-solid chromatography utilizes non-porous or porous graphitized carbon, enabling strong planar and π-electron interactions for selective adsorption and separation of aromatic and polar analytes. http://purl.obolibrary.org/obo/MS_1003728 gas chromatography system http://purl.obolibrary.org/obo/MS_1003737 separation system A gas chromatography (GC) system comprises an injector, temperature-controlled column with stationary phase, carrier gas supply, oven, and detector, enabling separation of volatile analytes. http://purl.obolibrary.org/obo/MS_1003729 two-dimensional gas chromatography system http://purl.obolibrary.org/obo/MS_1003728 gas chromatography system A two-dimensional gas chromatography system (GC×GC) uses orthogonal column sets connected by a modulator, providing enhanced separation of complex mixtures via sequential, independent mechanisms in primary and secondary columns. http://purl.obolibrary.org/obo/MS_1003730 gas chromatography system model http://purl.obolibrary.org/obo/MS_1003728 gas chromatography system Gas chromatography system model name not including the vendor's name. http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model http://purl.obolibrary.org/obo/MS_1003730 gas chromatography system model Agilent Technologies gas chromatography system model. http://purl.obolibrary.org/obo/MS_1003732 6890N http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model Agilent 6890N gas chromatograph. http://purl.obolibrary.org/obo/MS_1003733 gas chromatography mass spectrometry system http://purl.obolibrary.org/obo/MS_1003588 hyphenated separation system A gas chromatography mass spectrometry system (GC–MS) integrates a gas chromatograph for volatile analyte separation with a mass spectrometer for ionization and detection, enabling sensitive qualitative or quantitative analysis. http://purl.obolibrary.org/obo/MS_1003901 zero intensity point trimming http://purl.obolibrary.org/obo/MS_1000543 data processing action Apply an algorithm to remove excess zero intensity value data points from a spectrum. Data may be retained for interperatbility such as retaining only zeros that flank non-zero intensity value data points from a profile spectrum.. http://purl.obolibrary.org/obo/MS_1003902 zero intensity point trimming interpolation http://purl.obolibrary.org/obo/MS_1003901 zero intensity point trimming A zero intensity point trimming algorithm that interpolates the m/z coordinate values from the local data or an estimated model. http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A tandem instrument that combines two time-of-flight mass analyzers in series, where the first selects precursor ions and the second analyzes fragment ions produced by collision-induced dissociation or post-source decay. http://purl.obolibrary.org/obo/MS_1003948 fourier transform ion cyclotron resonance instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class An instrument that uses a Fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis. http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class An instrument that uses a magnetic sector mass analyzer as its primary means of mass analysis. http://purl.obolibrary.org/obo/MS_1003947 magnetic sector ion trap instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines a double-focusing magnetic sector analyzer for high-resolution precursor ion selection with an ion trap for MSn fragmentation analysis. http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class An instrument that uses a time-of-flight mass analyzer as its primary means of mass analysis. http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class An instrument that uses an ion trap mass analyzer as its primary means of mass analysis. http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class An instrument that uses a single quadrupole mass analyzer as its primary means of mass analysis. http://purl.obolibrary.org/obo/MS_1003812 lambda max http://purl.obolibrary.org/obo/MS_1003058 spectrum property The wavelength of maximum absorbance for a substance. This is analogous to the base peak m/z for UV-Vis spectroscopy. http://purl.obolibrary.org/obo/MS_1003813 list of doubles http://purl.obolibrary.org/obo/MS_1002710 list of type A list of xsd:double. http://purl.obolibrary.org/obo/MS_1003820 coordinate spacing model http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute Defines a model for calculating or correcting the spacing between points along a continuous dimension. http://purl.obolibrary.org/obo/MS_1003821 polynomial delta coordinate interpolation http://purl.obolibrary.org/obo/MS_1003820 coordinate spacing model A coordinate spacing model that predicts the next coordinate as a function of a low degree polynomial on the current coordinate, for instance a 2nd degree $x_{i + 1} = (a*x_i^2 + b*x_i + c) + x_i$. It is assumed that the parameters are inferred from the value list and the number implies the polynomial degree. http://purl.obolibrary.org/obo/MS_1003822 grid coordinate interpolation http://purl.obolibrary.org/obo/MS_1003820 coordinate spacing model A coordinate spacing model that uses some form of interpolation to calculate coordinate values between a fixed minimum and maximum value. This includes formula for (potentially lossily) converting a coordinate to an integer index and vice-versa. The grid model and recalibration function parameters are given by the value list. The recalibration function may be the identity function, or a more complex model defined in a child term. http://purl.obolibrary.org/obo/MS_1003824 linear grid interpolation http://purl.obolibrary.org/obo/MS_1003822 grid coordinate interpolation A coordinate spacing model that uses linear interpolation to map grid indices to coordinates $x_i = f_x(b + i * a)$ where $f$ is some recalibration function. http://purl.obolibrary.org/obo/MS_1003825 square root grid interpolation http://purl.obolibrary.org/obo/MS_1003822 grid coordinate interpolation A coordinate spacing model that maps grid indices to coordinates $x_i = f_x((b + i * a)^2)$ where $f$ is some recalibration function. The square root of the coordinate is linear with respect to the index. This mirrors the formula relating time-of-flight to m/z, $t = ksqrt{m/z}$ http://purl.obolibrary.org/obo/MS_1003826 coordinate grid encoding http://purl.obolibrary.org/obo/MS_1000572 binary data compression type This array stores indices or spans into some form of coordinate space model rather than the coordinates themselves, and that grid is stored externally from this data array. The objective being that these coordinates are more compact to store than the raw coordinates themselves. The value of this parameter is the grid identifier, if there are multiple to choose from. A separate coordinate spacing model parameter will signify what form of coordinate space model is used. http://purl.obolibrary.org/obo/MS_1003916 SpectroSwiss software http://purl.obolibrary.org/obo/MS_1000531 software SpectroSwiss software for mass spectrometry data processing and analysis. http://purl.obolibrary.org/obo/MS_1003917 Peak-by-Peak http://purl.obolibrary.org/obo/MS_1003916 SpectroSwiss software SpectroSwiss software for Fourier transform mass spectrometry (FTMS) data processing and analysis, providing advanced workflows including the processing of unreduced, transient data. http://purl.obolibrary.org/obo/MS_1003920 chromatographic column http://purl.obolibrary.org/obo/MS_1000857 run attribute A tube or housing containing a stationary phase, through which a mobile phase flows to achieve chromatographic separation of analytes. http://purl.obolibrary.org/obo/MS_1003921 liquid chromatographic column http://purl.obolibrary.org/obo/MS_1003945 chromatographic column type A chromatographic column designed for use with a liquid mobile phase, housing a stationary phase for analyte separation. http://purl.obolibrary.org/obo/MS_1003945 chromatographic column type http://purl.obolibrary.org/obo/MS_1000857 run attribute The type of chromatographic column classified by the mobile phase it is designed to operate with. http://purl.obolibrary.org/obo/MS_1003922 chromatographic stationary phase http://purl.obolibrary.org/obo/MS_1000857 run attribute The immobile phase in a chromatographic system with which analytes interact differentially, enabling separation based on chemical or physical properties. http://purl.obolibrary.org/obo/MS_1003923 chromatographic stationary phase attribute http://purl.obolibrary.org/obo/MS_1000857 run attribute Chromatographic stationary phase properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1003924 pore size http://purl.obolibrary.org/obo/MS_1003923 chromatographic stationary phase attribute The average diameter of the pores within the particles of the stationary phase, typically represented in angstroms (Å) http://purl.obolibrary.org/obo/MS_1003925 particle diameter http://purl.obolibrary.org/obo/MS_1003923 chromatographic stationary phase attribute The average diameter of the solid particles that constitute the stationary phase. http://purl.obolibrary.org/obo/MS_1003926 chromatographic column attribute http://purl.obolibrary.org/obo/MS_1000857 run attribute Properties of the chromatographic column hardware that are associated with a value. http://purl.obolibrary.org/obo/MS_1003927 column length http://purl.obolibrary.org/obo/MS_1003926 chromatographic column attribute The length of the chromatographic column, representing the path length available for separation. http://purl.obolibrary.org/obo/MS_1003928 column internal diameter http://purl.obolibrary.org/obo/MS_1003926 chromatographic column attribute The inner diameter of the chromatographic column. http://purl.obolibrary.org/obo/MS_1003929 particle porosity http://purl.obolibrary.org/obo/MS_1003923 chromatographic stationary phase attribute The porosity of the particles composing the chromatographic stationary phase. http://purl.obolibrary.org/obo/MS_1003930 fully porous http://purl.obolibrary.org/obo/MS_1003929 particle porosity A chromatographic stationary phase particle with pores distributed throughout its entire volume. http://purl.obolibrary.org/obo/MS_1003931 superficially porous http://purl.obolibrary.org/obo/MS_1003929 particle porosity A chromatographic stationary phase particle consisting of a solid, non-porous core surrounded by a porous shell. http://purl.obolibrary.org/obo/MS_1003932 non-porous http://purl.obolibrary.org/obo/MS_1003929 particle porosity A solid chromatographic stationary phase particle without internal pores. http://purl.obolibrary.org/obo/MS_1003933 support material http://purl.obolibrary.org/obo/MS_1003923 chromatographic stationary phase attribute The base material from which the chromatographic stationary phase is constructed. http://purl.obolibrary.org/obo/MS_1003934 silica-based http://purl.obolibrary.org/obo/MS_1003933 support material A chromatographic stationary phase constructed from silica particles, optionally with surface chemical modification. http://purl.obolibrary.org/obo/MS_1003935 hybrid particle http://purl.obolibrary.org/obo/MS_1003933 support material A chromatographic stationary phase constructed from organic-inorganic hybrid particles, such as ethylene-bridged hybrid (BEH), providing enhanced chemical stability and pH range. http://purl.obolibrary.org/obo/MS_1003936 polymer-based http://purl.obolibrary.org/obo/MS_1003933 support material A chromatographic stationary phase constructed from organic polymer particles such as polystyrene-divinylbenzene or methacrylate-based polymers. http://purl.obolibrary.org/obo/MS_1003937 monolithic http://purl.obolibrary.org/obo/MS_1003933 support material A chromatographic stationary phase consisting of a single continuous porous rod rather than packed discrete particles. http://purl.obolibrary.org/obo/MS_1003938 porous graphitic carbon http://purl.obolibrary.org/obo/MS_1003933 support material A chromatographic stationary phase composed of porous graphitic carbon, providing strong retention of polar compounds and chemical robustness across a wide pH range. http://purl.obolibrary.org/obo/MS_1003939 trap column http://purl.obolibrary.org/obo/MS_1003944 chromatographic column role A short chromatographic column used for on-line sample loading, concentration, and desalting prior to separation on the analytical column. http://purl.obolibrary.org/obo/MS_1003944 chromatographic column role http://purl.obolibrary.org/obo/MS_1000857 run attribute The functional role of a chromatographic column within the separation workflow. http://purl.obolibrary.org/obo/MS_1003940 guard column http://purl.obolibrary.org/obo/MS_1003944 chromatographic column role A short protective chromatographic column placed upstream of the analytical column to capture contaminants and extend analytical column lifetime. http://purl.obolibrary.org/obo/MS_1003941 analytical column http://purl.obolibrary.org/obo/MS_1003944 chromatographic column role The primary chromatographic column in which analyte separation occurs. http://purl.obolibrary.org/obo/MS_1003943 gas chromatographic column http://purl.obolibrary.org/obo/MS_1003945 chromatographic column type A chromatographic column designed for use with a gaseous mobile phase. http://purl.obolibrary.org/obo/MS_1003953 orbitrap instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class An instrument that uses an Orbitrap mass analyzer as its primary means of mass analysis. http://purl.obolibrary.org/obo/MS_1003954 argon gas cluster ion beam http://purl.obolibrary.org/obo/MS_1003959 gas cluster ion beam Argon gas cluster ion beam (Ar GCIB) bombardment uses a focused beam of large argon cluster ions, typically [Ar500]+ to [Ar10000]+, accelerated to high energies to sputter and generate secondary ions from a surface, enabling molecular depth profiling and imaging of organic and biological materials with reduced subsurface damage compared to monatomic ion beams. http://purl.obolibrary.org/obo/MS_1003959 gas cluster ion beam http://purl.obolibrary.org/obo/MS_1000446 fast ion bombardment A gas cluster ion beam (GCIB) is an ion source that generates and accelerates large aggregates of gas atoms or molecules to high energies. The low energy per constituent atom minimizes surface damage and molecular fragmentation, making it highly effective for molecular depth profiling and the analysis of fragile organic and biological materials. http://purl.obolibrary.org/obo/MS_1003955 singly charged bismuth trimer liquid metal ion gun http://purl.obolibrary.org/obo/MS_1003958 bismuth liquid metal ion gun A beam of singly charged bismuth trimer ([Bi3]+) ions for desorption and ionisation from a surface, providing high spatial resolution imaging and enhanced molecular secondary ion yields compared to monatomic primary ion beams. http://purl.obolibrary.org/obo/MS_1003958 bismuth liquid metal ion gun http://purl.obolibrary.org/obo/MS_1003960 liquid metal ion gun Bismuth liquid metal ion gun (Bi LMIG) bombardment uses a focused beam of bismuth ions emitted from a liquid metal ion source to desorb and ionize molecules from a surface. The LMIG source generates a diversity of monomers and clusters, which are filtered prior to the sample in order to select the specific ionisation characteristics. http://purl.obolibrary.org/obo/MS_1003956 doubly charged bismuth trimer liquid metal ion gun http://purl.obolibrary.org/obo/MS_1003958 bismuth liquid metal ion gun A beam of doubly charged bismuth trimer ([Bi3]2+) ions for desorption and ionisation from a surface. Ions achieve a higher velocity at a given acceleration voltage compared to singly charged [Bi3]+, resulting in enhanced secondary ion yields for surface analysis. http://purl.obolibrary.org/obo/MS_1003957 two-dimensional liquid chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Two-dimensional liquid chromatography (2D-LC) is a multidimensional separation technique that couples two liquid chromatography columns with different selectivities, such as strong cation exchange and reversed phase, connected by a switching valve or modulator to provide significantly higher peak capacity and resolving power for complex mixtures than one-dimensional liquid chromatography. http://purl.obolibrary.org/obo/MS_1003960 liquid metal ion gun http://purl.obolibrary.org/obo/MS_1000446 fast ion bombardment A liquid metal ion gun (LMIG) is an ion source that extracts and ionizes a thin layer of liquid metal from a fine heated needle using a high-voltage electric field. It produces a high-brightness, tightly focused beam of metal ions or clusters, enabling high-resolution imaging and analysis in Secondary Ion Mass Spectrometry (SIMS). http://purl.obolibrary.org/obo/UO_0000001 length unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the distance between two points. http://purl.obolibrary.org/obo/UO_0000002 mass unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the amount of matter/energy of a physical object. http://purl.obolibrary.org/obo/UO_0000003 time unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the dimension in which events occur in sequence. http://purl.obolibrary.org/obo/UO_0000005 temperature unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. http://purl.obolibrary.org/obo/UO_0000008 meter http://purl.obolibrary.org/obo/UO_0000045 base unit A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. http://purl.obolibrary.org/obo/UO_0000010 second http://purl.obolibrary.org/obo/UO_0000045 base unit A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. http://purl.obolibrary.org/obo/UO_0000016 millimeter http://purl.obolibrary.org/obo/UO_0000001 length unit A length unit which is equal to one thousandth of a meter or 10^[-3] m. http://purl.obolibrary.org/obo/UO_0000017 micrometer http://purl.obolibrary.org/obo/UO_0000001 length unit A length unit which is equal to one millionth of a meter or 10^[-6] m. http://purl.obolibrary.org/obo/UO_0000018 nanometer http://purl.obolibrary.org/obo/UO_0000001 length unit A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. http://purl.obolibrary.org/obo/UO_0000019 angstrom http://purl.obolibrary.org/obo/UO_0000001 length unit A length unit which is equal to 10 [-10] m. http://purl.obolibrary.org/obo/UO_0000021 gram http://purl.obolibrary.org/obo/UO_0000002 mass unit A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. http://purl.obolibrary.org/obo/UO_0000027 degree Celsius http://purl.obolibrary.org/obo/UO_0000005 temperature unit A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. http://purl.obolibrary.org/obo/UO_0000031 minute http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to 60 seconds. http://purl.obolibrary.org/obo/UO_0000095 volume unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. http://purl.obolibrary.org/obo/UO_0000098 milliliter http://purl.obolibrary.org/obo/UO_0000095 volume unit A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. http://purl.obolibrary.org/obo/UO_0000105 frequency unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the number of repetitive actions in a particular time. http://purl.obolibrary.org/obo/UO_0000106 hertz http://purl.obolibrary.org/obo/UO_0000105 frequency unit A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. http://purl.obolibrary.org/obo/UO_0000109 pressure unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the force applied to a given area. http://purl.obolibrary.org/obo/UO_0000175 gram per liter http://purl.obolibrary.org/obo/UO_0000052 mass density unit A mass unit density which is equal to mass of an object in grams divided by the volume in liters. http://purl.obolibrary.org/obo/UO_0000270 volumetric flow rate unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . http://purl.obolibrary.org/obo/UO_0000271 microliters per minute http://purl.obolibrary.org/obo/UO_0000270 volumetric flow rate unit A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. http://purl.obolibrary.org/obo/MS_1002826 MetaMorpheus http://purl.obolibrary.org/obo/MS_1001456 analysis software MetaMorpheus search engine. http://purl.obolibrary.org/obo/MS_1002827 MetaMorpheus:score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic MetaMorpheus score for PSMs. http://purl.obolibrary.org/obo/MS_1002828 MetaMorpheus:protein score http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups MetaMorpheus score for protein groups. http://purl.obolibrary.org/obo/MS_1002829 XCMS:into http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype Feature intensity produced by XCMS findPeaks() from integrated peak intensity. http://purl.obolibrary.org/obo/MS_1002830 XCMS:intf http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity. http://purl.obolibrary.org/obo/MS_1002831 XCMS:maxo http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype Feature intensity produced by XCMS findPeaks() from maximum peak intensity. http://purl.obolibrary.org/obo/MS_1002833 alternating polarity acquisition http://purl.obolibrary.org/obo/MS_1003776 acquisition polarity The scans of a run are acquired with polarities switching in a strictly alternating sequence (e.g., positive, negative, positive, negative), such that consecutive scans or scan cycles differ in polarity. http://purl.obolibrary.org/obo/MS_1002834 ProteomeDiscoverer:Delta Score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Delta Score reported by Proteome Discoverer version 2. http://purl.obolibrary.org/obo/MS_1002835 LTQ Orbitrap Classic http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Thermo Fisher Scientific LTQ Orbitrap Classic. http://purl.obolibrary.org/obo/MS_1002836 iProX dataset identifier http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. http://purl.obolibrary.org/obo/MS_1002837 iProX dataset URI http://purl.obolibrary.org/obo/MS_1000878 external reference identifier URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term http://purl.obolibrary.org/obo/PEFF_0000001 PEFF CV term CV term that may appear in a PEFF file header section. http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term http://purl.obolibrary.org/obo/PEFF_0000001 PEFF CV term CV term that may appear in a description line of a PEFF file individual sequence entry. http://purl.obolibrary.org/obo/PEFF_0000008 DbName http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the sequence database name. http://purl.obolibrary.org/obo/PEFF_0000009 Prefix http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the sequence database prefix. http://purl.obolibrary.org/obo/PEFF_0000010 DbDescription http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the sequence database short description. http://purl.obolibrary.org/obo/PEFF_0000011 Decoy http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the specifying whether the sequence database is a decoy database. http://purl.obolibrary.org/obo/PEFF_0000012 DbSource http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the source of the database file. http://purl.obolibrary.org/obo/PEFF_0000013 DbVersion http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the database version (release date) according to database provider. http://purl.obolibrary.org/obo/PEFF_0000014 DbDate http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider. http://purl.obolibrary.org/obo/PEFF_0000015 NumberOfEntries http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the sumber of sequence entries in the database. http://purl.obolibrary.org/obo/PEFF_0000016 Conversion http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the description of the conversion from original format to this current one. http://purl.obolibrary.org/obo/PEFF_0000017 SequenceType http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the molecular type of the sequences. http://purl.obolibrary.org/obo/PEFF_0000018 SpecificKey http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for database specific keywords not included in the current controlled vocabulary. http://purl.obolibrary.org/obo/PEFF_0000019 SpecificValue http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the specific values for a custom key. http://purl.obolibrary.org/obo/PEFF_0000020 DatabaseDescription http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the short description of the PEFF file. http://purl.obolibrary.org/obo/PEFF_0000021 GeneralComment http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for a general comment. http://purl.obolibrary.org/obo/PEFF_0000022 ProteoformDb http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms. http://purl.obolibrary.org/obo/PEFF_0000023 OptionalTagDef http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location. http://purl.obolibrary.org/obo/PEFF_0001001 DbUniqueId http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term Sequence database unique identifier. http://purl.obolibrary.org/obo/PEFF_0001002 PName http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the protein full name. http://purl.obolibrary.org/obo/PEFF_0001003 NcbiTaxId http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the NCBI taxonomy identifier. http://purl.obolibrary.org/obo/PEFF_0001004 TaxName http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the taxonomy name (latin or common name). http://purl.obolibrary.org/obo/PEFF_0001005 GName http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the gene name. http://purl.obolibrary.org/obo/PEFF_0001006 Length http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the sequence length. http://purl.obolibrary.org/obo/PEFF_0001007 SV http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the sequence version. http://purl.obolibrary.org/obo/PEFF_0001008 EV http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the entry version. http://purl.obolibrary.org/obo/PEFF_0001009 PE http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the Protein Evidence; A UniProtKB code 1-5. http://purl.obolibrary.org/obo/PEFF_0001010 Processed http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains. http://purl.obolibrary.org/obo/PEFF_0001011 Variant http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term OBSOLETE Sequence variation (substitution, insertion, deletion). http://purl.obolibrary.org/obo/PEFF_0001012 ModResPsi http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the modified residue with PSI-MOD identifier. http://purl.obolibrary.org/obo/PEFF_0001013 ModRes http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier. http://purl.obolibrary.org/obo/PEFF_0001014 AltAC http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the Alternative Accession Code. http://purl.obolibrary.org/obo/PEFF_0001015 SeqStatus http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the sequence status. Complete or Fragment. http://purl.obolibrary.org/obo/PEFF_0001016 CC http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the entry associated comment. http://purl.obolibrary.org/obo/PEFF_0001017 KW http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the entry associated keyword(s). http://purl.obolibrary.org/obo/PEFF_0001018 GO http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the Gene Ontology code. http://purl.obolibrary.org/obo/PEFF_0001019 XRef http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the cross-reference to an external resource. http://purl.obolibrary.org/obo/PEFF_0001020 mature protein http://purl.obolibrary.org/obo/PEFF_0001032 PEFF molecule processing keyword Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed. http://purl.obolibrary.org/obo/PEFF_0001021 signal peptide http://purl.obolibrary.org/obo/PEFF_0001032 PEFF molecule processing keyword Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein. http://purl.obolibrary.org/obo/PEFF_0001022 transit peptide http://purl.obolibrary.org/obo/PEFF_0001032 PEFF molecule processing keyword Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle. http://purl.obolibrary.org/obo/PEFF_0001023 Conflict http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the sequence conflict; a UniProtKB term. http://purl.obolibrary.org/obo/PEFF_0001024 Crc64 http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the Sequence checksum in crc64. http://purl.obolibrary.org/obo/PEFF_0001025 Domain http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the sequence range of a domain. http://purl.obolibrary.org/obo/PEFF_0001026 ID http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term. http://purl.obolibrary.org/obo/PEFF_0001027 ModResUnimod http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the modified residue with UniMod identifier. http://purl.obolibrary.org/obo/PEFF_0001028 VariantSimple http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term. http://purl.obolibrary.org/obo/PEFF_0001029 VariantComplex http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon. http://purl.obolibrary.org/obo/PEFF_1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment http://purl.obolibrary.org/obo/MS_1002479 regular expression ([0-9]+|[A-Z*](|.+)?). http://purl.obolibrary.org/obo/PEFF_1002002 regular expression for PEFF molecular sequence type http://purl.obolibrary.org/obo/MS_1002479 regular expression (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+). http://purl.obolibrary.org/obo/PEFF_1002003 regular expression for PEFF sequence status http://purl.obolibrary.org/obo/MS_1002479 regular expression (Complete|Fragment|[a-z0-9A-Z]+). http://purl.obolibrary.org/obo/MS_1002847 ProteomeCentral dataset URI http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter URI associated to one PX submission in ProteomeCentral. http://purl.obolibrary.org/obo/MS_1002865 Accepted manuscript http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet. http://purl.obolibrary.org/obo/MS_1002935 TopMG:fixed modification http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Fixed modifications for TopMG searching. http://purl.obolibrary.org/obo/MS_1002915 TopPIC:error tolerance http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Error tolerance for precursor and fragment masses in PPM. http://purl.obolibrary.org/obo/MS_1002954 collisional cross sectional area http://purl.obolibrary.org/obo/MS_1000861 molecular entity property Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry. http://purl.obolibrary.org/obo/MS_1003132 isoform-level identification statistic http://purl.obolibrary.org/obo/MS_1003131 isoform-level identification attribute Identification confidence metric for a isoform. http://purl.obolibrary.org/obo/MS_1003274 peak annotation confidence metric http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1. http://purl.obolibrary.org/obo/MS_1003275 other attribute name http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value http://purl.obolibrary.org/obo/MS_1003276 other attribute value http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name http://purl.obolibrary.org/obo/MS_1003277 value between -1 and 1 inclusive http://purl.obolibrary.org/obo/MS_1002304 domain range Value range for signed normalized score values. http://purl.obolibrary.org/obo/MS_1003278 m/z variability of peak http://purl.obolibrary.org/obo/MS_1003254 peak attribute A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte. http://purl.obolibrary.org/obo/MS_1003279 observation frequency of peak http://purl.obolibrary.org/obo/MS_1003254 peak attribute The frequency at which this peak is observed among replicate spectra of the same analyte. http://purl.obolibrary.org/obo/MS_1003280 intensity variability of peak http://purl.obolibrary.org/obo/MS_1003254 peak attribute A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte. http://purl.obolibrary.org/obo/MS_1003281 Casanovo http://purl.obolibrary.org/obo/MS_1001456 analysis software Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/. http://purl.obolibrary.org/obo/MS_1003282 Bruker TSF format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Bruker TSF raw file format. http://purl.obolibrary.org/obo/MS_1003283 Bruker TSF nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by frame=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1003284 Bruker TSF nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1003285 standard deviation of m/z values of peak among replicates http://purl.obolibrary.org/obo/MS_1003278 m/z variability of peak The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte. http://purl.obolibrary.org/obo/MS_1003286 coefficient of variation of intensity of peak among replicates http://purl.obolibrary.org/obo/MS_1003280 intensity variability of peak The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte. http://purl.obolibrary.org/obo/MS_1003287 standard deviation of intensity of peak among replicates http://purl.obolibrary.org/obo/MS_1003280 intensity variability of peak The standard deviation of the intensities of this peak among the replicate spectra of the same analyte. http://purl.obolibrary.org/obo/MS_1003288 number of unassigned peaks http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute The number of unassigned peaks in the spectrum. http://purl.obolibrary.org/obo/MS_1003289 intensity of highest unassigned peak http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute The intensity of the highest unassigned peak in the spectrum. http://purl.obolibrary.org/obo/MS_1003290 number of unassigned peaks among top 20 peaks http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute The number of unassigned peaks among the most intense 20 peaks in the spectrum. http://purl.obolibrary.org/obo/MS_1003409 Stellar http://purl.obolibrary.org/obo/MS_1003972 quadrupole ion trap instrument Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer. http://purl.obolibrary.org/obo/MS_1003400 rmzqc http://purl.obolibrary.org/obo/MS_1003399 quality control software An R package for reading, validating, and writing mzQC files. http://purl.obolibrary.org/obo/MS_1003399 quality control software http://purl.obolibrary.org/obo/MS_1001457 data processing software Software that creates or manipulates QC-related data. http://purl.obolibrary.org/obo/MS_1003401 jmzqc http://purl.obolibrary.org/obo/MS_1003399 quality control software A Java package for reading, validating, and writing mzQC files. http://purl.obolibrary.org/obo/MS_1003402 pymzqc http://purl.obolibrary.org/obo/MS_1003399 quality control software A Python package for reading, validating, and writing mzQC files. http://purl.obolibrary.org/obo/MS_1003403 InChI http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details IUPAC International Chemical Identifier. http://purl.obolibrary.org/obo/MS_1003404 timsTOF HT http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker Daltonics' timsTOF HT. http://purl.obolibrary.org/obo/MS_1003405 mzRecal http://purl.obolibrary.org/obo/MS_1001457 data processing software MS1 recalibration using identified peptides as internal calibrants. http://purl.obolibrary.org/obo/MS_1003406 spectrum clustering software http://purl.obolibrary.org/obo/MS_1000531 software Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte. http://purl.obolibrary.org/obo/MS_1003442 Orbitrap Astral Zoom http://purl.obolibrary.org/obo/MS_1003771 quadrupole orbitrap astral instrument Thermo Scientific Orbitrap Astral Zoom mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and an Astral analyzer. http://purl.obolibrary.org/obo/MS_1003683 Thermo Scientific liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model Thermo Scientific liquid chromatography system model. http://purl.obolibrary.org/obo/MS_1003684 Accela http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Accela UHPLC system. http://purl.obolibrary.org/obo/MS_1003685 Accela II http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Accela II UHPLC system. http://purl.obolibrary.org/obo/MS_1003686 Dionex Integrion HPIC http://purl.obolibrary.org/obo/MS_1003683 Thermo Scientific liquid chromatography system model Thermo Dionex Integrion HPIC ion chromatography system. http://purl.obolibrary.org/obo/MS_1003687 Dionex Integrion RFIC http://purl.obolibrary.org/obo/MS_1003683 Thermo Scientific liquid chromatography system model Thermo Dionex Integrion RFIC ion chromatography system. http://purl.obolibrary.org/obo/MS_1003688 Dionex UltiMate 3000 RSLC http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Dionex UltiMate 3000 RSLC UHPLC system. http://purl.obolibrary.org/obo/MS_1003689 Dionex UltiMate 3000 RSLCnano http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Dionex UltiMate 3000 RSLCnano UHPLC system. http://purl.obolibrary.org/obo/MS_1003690 Dionex UltiMate 3000 http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Dionex UltiMate 3000 UHPLC system. http://purl.obolibrary.org/obo/MS_1003691 Dionex UltiMate 3000 XRS http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Dionex UltiMate 3000 XRS UHPLC system. http://purl.obolibrary.org/obo/MS_1003692 EASY-nLC 1000 http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo EASY-nLC 1000 UHPLC system. http://purl.obolibrary.org/obo/MS_1003693 EASY-nLC 1200 http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo EASY-nLC 1200 UHPLC system. http://purl.obolibrary.org/obo/MS_1003694 Surveyor http://purl.obolibrary.org/obo/MS_1003590 high-performance liquid chromatography system Thermo Surveyor HPLC system. http://purl.obolibrary.org/obo/MS_1003695 Vanquish Duo http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Vanquish Duo UHPLC system. http://purl.obolibrary.org/obo/MS_1003696 Vanquish Flex http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Vanquish Flex UHPLC system. http://purl.obolibrary.org/obo/MS_1003697 Vanquish Horizon http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Vanquish Horizon UHPLC system. http://purl.obolibrary.org/obo/MS_1003698 Vanquish http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Vanquish UHPLC system. http://purl.obolibrary.org/obo/MS_1003699 Dionex ICS-5000+ http://purl.obolibrary.org/obo/MS_1003683 Thermo Scientific liquid chromatography system model Thermo Dionex ICS-5000+ ion chromatography system. http://purl.obolibrary.org/obo/MS_1003700 Proxeon EASY-nLC II http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Proxeon EASY-nLC II UHPLC system. http://purl.obolibrary.org/obo/MS_1003701 Cohesive Technologies TX2 http://purl.obolibrary.org/obo/MS_1003590 high-performance liquid chromatography system Thermo Cohesive Technologies TX2 HPLC system. http://purl.obolibrary.org/obo/MS_1003702 Rheos Allegro http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system Thermo Flux Instruments Rheos Allegro UHPLC pump. http://purl.obolibrary.org/obo/MS_1003703 Rheos 2000 Micro http://purl.obolibrary.org/obo/MS_1003590 high-performance liquid chromatography system Thermo Flux Instruments Rheos 2000 Micro HPLC pump. http://purl.obolibrary.org/obo/MS_1003704 Rheos 2200 Micro http://purl.obolibrary.org/obo/MS_1003590 high-performance liquid chromatography system Thermo Flux Instruments Rheos 2200 Micro HPLC pump. http://purl.obolibrary.org/obo/MS_1003705 1525 Micro http://purl.obolibrary.org/obo/MS_1003590 high-performance liquid chromatography system Waters 1525 Micro HPLC pump. http://purl.obolibrary.org/obo/MS_1003706 ACQUITY Premier http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters ACQUITY Premier UPLC system. http://purl.obolibrary.org/obo/MS_1003707 ACQUITY UPLC H-Class PLUS http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters ACQUITY UPLC H-Class PLUS UPLC system. http://purl.obolibrary.org/obo/MS_1003708 ACQUITY UPLC I-Class PLUS http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters ACQUITY UPLC I-Class PLUS UPLC system. http://purl.obolibrary.org/obo/MS_1003709 ACQUITY UPLC M-Class http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model Waters ACQUITY UPLC M-Class UPLC system. http://purl.obolibrary.org/obo/MS_1003710 Alliance 2695 Separations Module http://purl.obolibrary.org/obo/MS_1003590 high-performance liquid chromatography system Waters Alliance 2695 Separations Module HPLC system. http://purl.obolibrary.org/obo/MS_1003780 zstd compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Zstandard compression, a fast, modern, general purpose lossless compression algorithm. http://purl.obolibrary.org/obo/MS_1003781 byte-shuffled zstd compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Byte shuffle transform followed by Zstandard compression. http://purl.obolibrary.org/obo/MS_1003782 dictionary-encoded zstd compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Dictionary encoding followed by Zstandard compression using a sorted dictionary with separately byte-shuffled values and indices. http://purl.obolibrary.org/obo/MS_1003783 MS-Numpress linear prediction compression followed by zstd compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression using MS-Numpress linear prediction compression and Zstandard . http://purl.obolibrary.org/obo/MS_1003784 MS-Numpress positive integer compression followed by zstd compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression using MS-Numpress positive integer compression and Zstandard. http://purl.obolibrary.org/obo/MS_1003785 MS-Numpress short logged float compression followed by zstd compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression using MS-Numpress short logged float compression and Zstandard. http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter http://purl.obolibrary.org/obo/MS_1001458 spectrum generation information Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam. http://purl.obolibrary.org/obo/MS_1003004 maXis II http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker Daltonics' maXis II. http://purl.obolibrary.org/obo/MS_1003005 timsTOF Pro http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker Daltonics' timsTOF Pro. http://purl.obolibrary.org/obo/MS_1003006 mean inverse reduced ion mobility array http://purl.obolibrary.org/obo/MS_1002893 ion mobility array Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. http://purl.obolibrary.org/obo/MS_1003007 raw ion mobility array http://purl.obolibrary.org/obo/MS_1002893 ion mobility array Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. http://purl.obolibrary.org/obo/MS_1003008 raw inverse reduced ion mobility array http://purl.obolibrary.org/obo/MS_1002893 ion mobility array Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. http://purl.obolibrary.org/obo/MS_1003009 Shimadzu Biotech LCD format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Shimadzu Biotech LCD file format. http://purl.obolibrary.org/obo/PEFF_0001035 initiator methionine http://purl.obolibrary.org/obo/PEFF_0001032 PEFF molecule processing keyword N-terminal methionine residue of a protein that can be co-translationally cleaved. http://purl.obolibrary.org/obo/MS_1003207 library creation software http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Library creation software http://purl.obolibrary.org/obo/MS_1003208 experimental precursor monoisotopic m/z http://purl.obolibrary.org/obo/MS_1003295 summary statistics of replicates The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum. http://purl.obolibrary.org/obo/MS_1003209 monoisotopic m/z deviation http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum. http://purl.obolibrary.org/obo/MS_1003210 average m/z deviation http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum. http://purl.obolibrary.org/obo/MS_1003211 library spectrum attribute set http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library http://purl.obolibrary.org/obo/MS_1003213 mass spectrometry acquisition method http://purl.obolibrary.org/obo/MS_1001954 acquisition parameter Mode of running a mass spectrometer method by which mass ranges are selected and possibly dissociated. http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect http://purl.obolibrary.org/obo/MS_1001458 spectrum generation information Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated. http://purl.obolibrary.org/obo/MS_1003215 data-independent acquisition http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions. http://purl.obolibrary.org/obo/MS_1003216 dissociation of full mass range http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once.. http://purl.obolibrary.org/obo/MS_1003217 dissociation of scanning quadrupole across a specified mass range http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect Mass spectrometer data acquisition method wherein a quadrupole mass analyzer transmits a sliding window of precursor ions for dissociation and spectrum acquisition within each acquisition cycle. This correlates precursor selection with product ion detection resulting in 'quadrupole transmission window' as an additional dimension in the resulting data. An example of such an approach is Waters SONAR. http://purl.obolibrary.org/obo/MS_1003218 dissociation of sequential mass ranges http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured. http://purl.obolibrary.org/obo/MS_1003219 ion mobility separation http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement. http://purl.obolibrary.org/obo/MS_1003220 adduct deconvolution http://purl.obolibrary.org/obo/MS_1000543 data processing action Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule. http://purl.obolibrary.org/obo/MS_1003221 data-dependent acquisition http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run. http://purl.obolibrary.org/obo/MS_1003222 ion mobility deconvolution http://purl.obolibrary.org/obo/MS_1000543 data processing action Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte. http://purl.obolibrary.org/obo/MS_1003224 data independent acquisition from dissociation of sequential mass ranges http://purl.obolibrary.org/obo/MS_1003218 dissociation of sequential mass ranges Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC. http://purl.obolibrary.org/obo/MS_1003225 data independent acquisition from dissociation of sequential mass ranges after ion mobility separation http://purl.obolibrary.org/obo/MS_1003219 ion mobility separation Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF. http://purl.obolibrary.org/obo/MS_1003226 data independent acquisition from dissociation of full mass range after ion mobility separation http://purl.obolibrary.org/obo/MS_1003219 ion mobility separation Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF. http://purl.obolibrary.org/obo/MS_1003227 data independent acquisition from dissociation of full mass range http://purl.obolibrary.org/obo/MS_1003219 ion mobility separation Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID. http://purl.obolibrary.org/obo/MS_1003228 data independent acquisition from dissociation of scanning quadrupole across mass range http://purl.obolibrary.org/obo/MS_1003217 dissociation of scanning quadrupole across a specified mass range Data independent mass spectrometer acquisition method wherein a quadrupole mass analyzer transmits a sliding window of precursor ions for dissociation and spectrum acquisition within each acquisition cycle. This correlates precursor selection with product ion detection resulting in 'quadrupole transmission window' as an additional dimension in the resulting data. An example of such an approach is Waters SONAR. http://purl.obolibrary.org/obo/MS_1003229 timsTOF http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker Daltonics' timsTOF. http://purl.obolibrary.org/obo/MS_1003230 timsTOF Pro 2 http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker Daltonics' timsTOF Pro 2. http://purl.obolibrary.org/obo/MS_1003231 timsTOF SCP http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker Daltonics' timsTOF SCP. http://purl.obolibrary.org/obo/MS_4000003 single value http://purl.obolibrary.org/obo/MS_4000002 QC metric value type Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). http://purl.obolibrary.org/obo/MS_4000004 n-tuple http://purl.obolibrary.org/obo/MS_4000002 QC metric value type Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable). http://purl.obolibrary.org/obo/MS_4000005 table http://purl.obolibrary.org/obo/MS_4000002 QC metric value type Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). http://purl.obolibrary.org/obo/MS_4000006 matrix http://purl.obolibrary.org/obo/MS_4000002 QC metric value type A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable). http://purl.obolibrary.org/obo/MS_4000008 ID based metric http://purl.obolibrary.org/obo/MS_4000007 QC metric category QC metric based on identification results. http://purl.obolibrary.org/obo/MS_4000009 ID free metric http://purl.obolibrary.org/obo/MS_4000007 QC metric category QC metric not based on identification results. http://purl.obolibrary.org/obo/MS_4000010 quantification based metric http://purl.obolibrary.org/obo/MS_4000007 QC metric category QC metric based on quantification results. http://purl.obolibrary.org/obo/MS_4000012 single run based metric http://purl.obolibrary.org/obo/MS_4000007 QC metric category QC metric calculated from a single run (e.g. one .raw file). http://purl.obolibrary.org/obo/MS_4000013 multiple runs based metric http://purl.obolibrary.org/obo/MS_4000007 QC metric category QC metric calculated from multiple runs (e.g. multiple .raw files). http://purl.obolibrary.org/obo/MS_4000014 single spectrum based metric http://purl.obolibrary.org/obo/MS_4000007 QC metric category QC metric calculated from a single spectrum. http://purl.obolibrary.org/obo/MS_4000015 multiple spectra based metric http://purl.obolibrary.org/obo/MS_4000007 QC metric category QC metric calculated from multiple spectra. http://purl.obolibrary.org/obo/MS_4000016 retention time metric http://purl.obolibrary.org/obo/MS_4000001 QC metric QC metric related to retention time. http://purl.obolibrary.org/obo/MS_4000017 chromatogram metric http://purl.obolibrary.org/obo/MS_4000001 QC metric QC metric related to a chromatogram. http://purl.obolibrary.org/obo/MS_4000018 XIC metric http://purl.obolibrary.org/obo/MS_4000017 chromatogram metric QC metric related to an extracted ion chromatogram. http://purl.obolibrary.org/obo/MS_4000019 MS metric http://purl.obolibrary.org/obo/MS_4000001 QC metric QC metric related to the mass spectrometry acquisition. http://purl.obolibrary.org/obo/MS_4000020 ion source metric http://purl.obolibrary.org/obo/MS_4000019 MS metric QC metric related to events in the ion source. http://purl.obolibrary.org/obo/MS_4000021 MS1 metric http://purl.obolibrary.org/obo/MS_4000019 MS metric QC metric based on MS1 events. http://purl.obolibrary.org/obo/MS_4000022 MS2 metric http://purl.obolibrary.org/obo/MS_4000019 MS metric QC metric based on MS2 events. http://purl.obolibrary.org/obo/MS_4000023 sample preparation metric http://purl.obolibrary.org/obo/MS_4000001 QC metric QC metric related to the sample preparation. http://purl.obolibrary.org/obo/MS_4000024 environment metric http://purl.obolibrary.org/obo/MS_4000001 QC metric QC metric related to measurements of the ambient environment, such as the laboratory. http://purl.obolibrary.org/obo/MS_4000050 XIC50 fraction http://purl.obolibrary.org/obo/MS_4000003 single value The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC. http://purl.obolibrary.org/obo/MS_4000051 XIC-FWHM quantiles http://purl.obolibrary.org/obo/MS_4000004 n-tuple The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of XIC-FWHM-Q1,Q2,Q3. http://purl.obolibrary.org/obo/MS_4000052 obsolete XIC-Height quartile ratios http://purl.obolibrary.org/obo/MS_4000004 n-tuple OBSOLETE. The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3. http://purl.obolibrary.org/obo/MS_4000053 chromatography duration http://purl.obolibrary.org/obo/MS_4000003 single value The retention time duration of the chromatography in seconds. http://purl.obolibrary.org/obo/MS_4000054 obsolete TIC quarters RT fraction http://purl.obolibrary.org/obo/MS_4000004 n-tuple OBSOLETE. The interval when the respective quarter of the TIC accumulates divided by retention time duration. http://purl.obolibrary.org/obo/MS_4000055 obsolete MS1 quarter RT fraction http://purl.obolibrary.org/obo/MS_4000004 n-tuple OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration. http://purl.obolibrary.org/obo/MS_4000056 obsolete MS2 quarter RT fraction http://purl.obolibrary.org/obo/MS_4000004 n-tuple OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration. http://purl.obolibrary.org/obo/MS_4000057 obsolete MS1 TIC-change quartile ratios http://purl.obolibrary.org/obo/MS_4000004 n-tuple OBSOLETE. The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3 http://purl.obolibrary.org/obo/MS_4000058 obsolete MS1 TIC quartile ratios http://purl.obolibrary.org/obo/MS_4000004 n-tuple OBSOLETE. The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. http://purl.obolibrary.org/obo/MS_4000059 number of MS1 spectra http://purl.obolibrary.org/obo/MS_4000003 single value The number of MS1 events in the run. http://purl.obolibrary.org/obo/MS_4000060 number of MS2 spectra http://purl.obolibrary.org/obo/MS_4000003 single value The number of MS2 events in the run. http://purl.obolibrary.org/obo/MS_4000061 MS1 density quantiles http://purl.obolibrary.org/obo/MS_4000004 n-tuple The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000062 MS2 density quantiles http://purl.obolibrary.org/obo/MS_4000004 n-tuple The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000063 MS2 known precursor charges fractions http://purl.obolibrary.org/obo/MS_4000005 table The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher. http://purl.obolibrary.org/obo/MS_4000064 MS2 unknown and likely precursor charges fractions http://purl.obolibrary.org/obo/MS_4000005 table The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states. http://purl.obolibrary.org/obo/MS_4000065 fastest frequency for MS level 1 collection http://purl.obolibrary.org/obo/MS_4000003 single value Fastest frequency for MS level 1 collection http://purl.obolibrary.org/obo/MS_4000066 fastest frequency for MS level 2 collection http://purl.obolibrary.org/obo/MS_4000003 single value Fastest frequency for MS level 2 collection http://purl.obolibrary.org/obo/MS_4000067 MS run duration http://purl.obolibrary.org/obo/MS_4000003 single value The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds. http://purl.obolibrary.org/obo/MS_4000177 contaminant protein abundance fraction http://purl.obolibrary.org/obo/MS_4000003 single value The fraction of total protein abundance in a mass spectrometry run or a group of runs which can be attributed to a user-defined list of contaminant proteins (e.g. using the cRAP contaminant database). http://purl.obolibrary.org/obo/MS_4000195 DIA isolation window m/z widths http://purl.obolibrary.org/obo/MS_4000004 n-tuple The minimum and maximum m/z width of the DIA isolation windows, defined as the subtraction between the high m/z boundary and the low m/z boundary. For fixed-window DIA methods, the same value is reported twice. http://purl.obolibrary.org/obo/MS_4000200 run outlier score PCA distance http://purl.obolibrary.org/obo/MS_4000005 table Outlier score for MS runs based on the median Euclidean distance for each run to every other run after robust PCA transformation of the QC metrics for all runs. http://purl.obolibrary.org/obo/MS_1003786 electrophoretic separation http://purl.obolibrary.org/obo/MS_1000857 run attribute Electrophoretic separation is a technique in which charged analytes are separated by differential migration in an applied electric field. http://purl.obolibrary.org/obo/MS_1003787 capillary electrophoresis http://purl.obolibrary.org/obo/MS_1003786 electrophoretic separation Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility. http://purl.obolibrary.org/obo/MS_1003788 electrochromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Electrochromatography is a liquid chromatography technique in which the mobile phase is driven through a stationary phase by electroosmotic flow generated by an applied electric field, combining electrophoretic migration with chromatographic retention. http://purl.obolibrary.org/obo/MS_1003789 ion-pair reversed phase chromatography http://purl.obolibrary.org/obo/MS_1003582 reversed phase chromatography Ion-pair reversed-phase chromatography is a reversed-phase chromatography technique in which an ion-pairing reagent is added to the mobile phase to enable retention and separation of charged or ionizable analytes on a nonpolar stationary phase. http://purl.obolibrary.org/obo/MS_1003790 supercritical fluid chromatography http://purl.obolibrary.org/obo/MS_1002270 chromatography separation Supercritical fluid chromatography (SFC) is a separation technique in which the mobile phase is a fluid above and relatively close to its critical temperature and pressure. http://purl.obolibrary.org/obo/UO_0000190 ratio http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. http://purl.obolibrary.org/obo/UO_0000121 angle unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the figure or space formed by the junction of two lines or planes. http://purl.obolibrary.org/obo/UO_0000122 plane angle unit http://purl.obolibrary.org/obo/UO_0000121 angle unit A unit which is a standard measure of the angle formed by two straight lines in the same plane. http://purl.obolibrary.org/obo/UO_0000150 nanosecond http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s. http://purl.obolibrary.org/obo/UO_0000182 density unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the influence exerted by some mass. http://purl.obolibrary.org/obo/UO_0000185 degree http://purl.obolibrary.org/obo/UO_0000122 plane angle unit A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad. http://purl.obolibrary.org/obo/UO_0000191 fraction http://purl.obolibrary.org/obo/UO_0000190 ratio A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). http://purl.obolibrary.org/obo/UO_0000217 electric potential difference unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field. http://purl.obolibrary.org/obo/UO_0000047 area unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of the amount of a 2-dimensional flat surface. http://purl.obolibrary.org/obo/NCIT_C21514 Temporal Qualifier http://purl.obolibrary.org/obo/NCIT_C41009 Qualifier Terms used to indicate units of time or other terms associated with time. http://purl.obolibrary.org/obo/NCIT_C45781 Density http://purl.obolibrary.org/obo/NCIT_C25447 Characteristic The amount of something per unit size. http://purl.obolibrary.org/obo/MS_1002953 TopMG:spectral p-value http://purl.obolibrary.org/obo/MS_1002352 PSM-level p-value TopMG spectrum-level p-value. http://purl.obolibrary.org/obo/MS_1002904 proteoform-level identification attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Proteoform level information. http://purl.obolibrary.org/obo/MS_1003398 deconvoluted data http://purl.obolibrary.org/obo/MS_1000524 data file content The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file. http://purl.obolibrary.org/obo/MS_1002958 isotopologue MS peak http://purl.obolibrary.org/obo/MS_1002956 isotopic ion MS peak The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'. http://purl.obolibrary.org/obo/MS_1002930 TopPIC:proteoform-level FDR http://purl.obolibrary.org/obo/MS_1002906 search engine specific score for proteoforms TopPIC proteoform-level FDR. http://purl.obolibrary.org/obo/MS_1002986 in-solution digestion http://purl.obolibrary.org/obo/MS_1000831 sample preparation Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes. http://purl.obolibrary.org/obo/MS_1002911 proteoform-level local FDR threshold http://purl.obolibrary.org/obo/MS_1002909 proteoform-level statistical threshold Threshold for the local false discovery rate of proteoforms. http://purl.obolibrary.org/obo/MS_4000178 precursor ppm deviation mean http://purl.obolibrary.org/obo/MS_4000003 single value The mean of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied http://purl.obolibrary.org/obo/MS_1003434 AlphaLP http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name A serine protease that hydrolyzes peptide bonds at the C-terminus of threonine, alanine, serine, and valine. (EC:3.4.21.12) http://purl.obolibrary.org/obo/MS_1003435 (?<=[TSAV]) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for alphaLP. http://purl.obolibrary.org/obo/MS_4000196 DIA isolation window count http://purl.obolibrary.org/obo/MS_4000004 n-tuple The minimum and maximum number of times any specific DIA isolation window is measured via MS/MS. In case all isolation windows are sampled the same number of times, this value is reported twice. http://purl.obolibrary.org/obo/PEFF_0001036 PSequence http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the peptide sequence. http://purl.obolibrary.org/obo/MS_1002756 iodoTMT quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow. http://purl.obolibrary.org/obo/MS_1002757 glyco-TMT quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow. http://purl.obolibrary.org/obo/MS_1002758 aminoxyTMT quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow. http://purl.obolibrary.org/obo/MS_1002759 hydrazideTMT quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow. http://purl.obolibrary.org/obo/MS_1002760 iTRAQH quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow. http://purl.obolibrary.org/obo/MS_1002761 DiART quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow. http://purl.obolibrary.org/obo/MS_1002762 DiLeu quantitation analysis http://purl.obolibrary.org/obo/MS_1002009 isobaric label quantitation analysis Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow. http://purl.obolibrary.org/obo/MS_1002763 TMT reagent 127N http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 127N. http://purl.obolibrary.org/obo/MS_1002764 TMT reagent 127C http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 127C. http://purl.obolibrary.org/obo/MS_1002765 TMT reagent 128N http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 128N. http://purl.obolibrary.org/obo/MS_1002766 TMT reagent 128C http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 128C. http://purl.obolibrary.org/obo/MS_1002767 TMT reagent 129N http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 129N. http://purl.obolibrary.org/obo/MS_1002768 TMT reagent 129C http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 129C. http://purl.obolibrary.org/obo/MS_1002769 TMT reagent 130N http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 130N. http://purl.obolibrary.org/obo/MS_1002770 TMT reagent 130C http://purl.obolibrary.org/obo/MS_1002615 TMT reagent The name of the sample labelled with the TMT reagent 130C. http://purl.obolibrary.org/obo/MS_1002771 DiART reagent http://purl.obolibrary.org/obo/MS_1002602 sample label Deuterium isobaric amine reactive tag labeling reagent. http://purl.obolibrary.org/obo/MS_1002772 DiART reagent 114 http://purl.obolibrary.org/obo/MS_1002771 DiART reagent The name of the sample labelled with the DiART reagent 114. http://purl.obolibrary.org/obo/MS_1002773 DiART reagent 115 http://purl.obolibrary.org/obo/MS_1002771 DiART reagent The name of the sample labelled with the DiART reagent 115. http://purl.obolibrary.org/obo/MS_1002774 DiART reagent 116 http://purl.obolibrary.org/obo/MS_1002771 DiART reagent The name of the sample labelled with the DiART reagent 116. http://purl.obolibrary.org/obo/MS_1002775 DiART reagent 117 http://purl.obolibrary.org/obo/MS_1002771 DiART reagent The name of the sample labelled with the DiART reagent 117. http://purl.obolibrary.org/obo/MS_1002776 DiART reagent 118 http://purl.obolibrary.org/obo/MS_1002771 DiART reagent The name of the sample labelled with the DiART reagent 118. http://purl.obolibrary.org/obo/MS_1002777 DiART reagent 119 http://purl.obolibrary.org/obo/MS_1002771 DiART reagent The name of the sample labelled with the DiART reagent 119. http://purl.obolibrary.org/obo/MS_1002778 DiLeu reagent http://purl.obolibrary.org/obo/MS_1002602 sample label Dimethyl leucine labeling reagent. http://purl.obolibrary.org/obo/MS_1002779 DiLeu reagent 115 http://purl.obolibrary.org/obo/MS_1002778 DiLeu reagent The name of the sample labelled with the DiLeu reagent 115. http://purl.obolibrary.org/obo/MS_1002780 DiLeu reagent 116 http://purl.obolibrary.org/obo/MS_1002778 DiLeu reagent The name of the sample labelled with the DiLeu reagent 116. http://purl.obolibrary.org/obo/MS_1002781 DiLeu reagent 117 http://purl.obolibrary.org/obo/MS_1002778 DiLeu reagent The name of the sample labelled with the DiLeu reagent 117. http://purl.obolibrary.org/obo/MS_1002782 DiLeu reagent 118 http://purl.obolibrary.org/obo/MS_1002778 DiLeu reagent The name of the sample labelled with the DiLeu reagent 118. http://purl.obolibrary.org/obo/MS_1002852 Dataset FTP location http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter FTP location of one entire PX data set. http://purl.obolibrary.org/obo/MS_1002896 compound identification confidence level http://purl.obolibrary.org/obo/MS_1002895 small molecule identification attribute Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'. http://purl.obolibrary.org/obo/MS_1002922 TopPIC:proteoform-level cutoff value http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Proteoform-level cutoff value for filtering identified proteoform spectrum matches. http://purl.obolibrary.org/obo/MS_1002987 IdentiPy http://purl.obolibrary.org/obo/MS_1001456 analysis software IdentiPy. http://purl.obolibrary.org/obo/MS_1003096 Orbitrap Velos Pro http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro. http://purl.obolibrary.org/obo/MS_1003410 electron beam energy http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute The kinetic energy of the electron beam used in dissociation methods induced by a free electron beam, such as electron-capture dissociation (ECD), electron-detachment dissociation (EDD), and electron-activated dissociation (EAD). http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A tandem instrument that employs three quadrupoles in series, where the first (Q1) acts as a mass filter for precursor ion selection, the second (q2) serves as a collision cell for fragmentation, and the third (Q3) as a mass filter for product ion detection. http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines a quadrupole mass filter, an ion mobility spectrometry separation cell, and a time-of-flight mass analyzer, enabling separation of ions by size and shape in addition to mass-to-charge ratio. http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with a time-of-flight mass analyzer for high-resolution, accurate-mass detection of product ions. http://purl.obolibrary.org/obo/MS_1003764 ion trap time-of-flight instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines an ion trap for ion accumulation, storage, and fragmentation with a time-of-flight mass analyzer for high-resolution, accurate-mass detection. http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines a triple quadrupole configuration with a linear ion trap, where the third quadrupole can function either as a conventional mass filter or as a linear ion trap for MSn analysis. http://purl.obolibrary.org/obo/MS_1003766 quadrupole fourier transform ion cyclotron resonance instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines a quadrupole for ion guiding or mass filtering with a Fourier transform ion cyclotron resonance mass analyzer for ultra-high resolution and mass accuracy. http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass detection. http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with an Orbitrap mass analyzer for high-resolution, accurate-mass detection. http://purl.obolibrary.org/obo/MS_1003770 quadrupole ion trap orbitrap instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines a quadrupole mass filter, a linear ion trap for MSn fragmentation, and an Orbitrap mass analyzer for high-resolution, accurate-mass detection. http://purl.obolibrary.org/obo/MS_1003771 quadrupole orbitrap astral instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class A hybrid instrument that combines a quadrupole mass filter, an Orbitrap mass analyzer, and an asymmetric track lossless (ASTRAL) analyzer for high-resolution analysis and high-speed MS/MS measurements. http://purl.obolibrary.org/obo/MS_1003801 AccurateMassSearch http://purl.obolibrary.org/obo/MS_1000752 TOPP software OpenMS TOPP tool to assemble metabolite features from singleton mass traces. http://purl.obolibrary.org/obo/UO_0000218 volt http://purl.obolibrary.org/obo/UO_0000217 electric potential difference unit An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy. http://purl.obolibrary.org/obo/MS_1002822 OpenMS file format http://purl.obolibrary.org/obo/MS_1001459 file format File format developed by the OpenMS team. http://purl.obolibrary.org/obo/MS_1002823 idXML http://purl.obolibrary.org/obo/MS_1002822 OpenMS file format OpenMS intermediate identification format. http://purl.obolibrary.org/obo/MS_1002824 featureXML http://purl.obolibrary.org/obo/MS_1002822 OpenMS file format OpenMS feature file format. http://purl.obolibrary.org/obo/MS_1002825 consensusXML http://purl.obolibrary.org/obo/MS_1002822 OpenMS file format OpenMS consensus map format. http://purl.obolibrary.org/obo/MS_1002939 TopMG:spectral cutoff type http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Spectrum-level cutoff type for filtering identified proteoform spectrum matches. http://purl.obolibrary.org/obo/MS_1002940 TopMG:spectral cutoff value http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Spectrum-level cutoff value for filtering identified proteoform spectrum matches. http://purl.obolibrary.org/obo/MS_1003134 ProSight:isoform Q-value http://purl.obolibrary.org/obo/MS_1003133 isoform-level Q-value ProSight isoform-level Q-value. http://purl.obolibrary.org/obo/MS_1003135 ProSight:protein Q-value http://purl.obolibrary.org/obo/MS_1001869 protein-level q-value ProSight protein-level Q-value. http://purl.obolibrary.org/obo/MS_1003133 isoform-level Q-value http://purl.obolibrary.org/obo/MS_1003132 isoform-level identification statistic Estimation of the Q-value for isoforms. http://purl.obolibrary.org/obo/MS_1002707 (?=[KR]) http://purl.obolibrary.org/obo/MS_1001180 Cleavage agent regular expression Regular expression for LysargiNase. http://purl.obolibrary.org/obo/MS_1002708 LysargiNase http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues. http://purl.obolibrary.org/obo/MS_1002710 list of type http://purl.obolibrary.org/obo/MS_1002709 compound data type A data type defining a list of values of a single type. http://purl.obolibrary.org/obo/MS_1002711 list of strings http://purl.obolibrary.org/obo/MS_1002710 list of type A list of xsd:string. http://purl.obolibrary.org/obo/MS_1002712 list of integers http://purl.obolibrary.org/obo/MS_1002710 list of type A list of xsd:integer. http://purl.obolibrary.org/obo/MS_1002713 list of floats http://purl.obolibrary.org/obo/MS_1002710 list of type A list of xsd:float. http://purl.obolibrary.org/obo/MS_1003092 number of mantissa bits truncated http://purl.obolibrary.org/obo/MS_1003091 binary data compression parameter Number of extraneous mantissa bits truncated to improve subsequent compression. http://purl.obolibrary.org/obo/MS_1003094 Orbitrap Exploris 240 http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS. http://purl.obolibrary.org/obo/MS_1003095 Orbitrap Exploris 120 http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS. http://purl.obolibrary.org/obo/MS_1003097 MaxQuant protein group-level score http://purl.obolibrary.org/obo/MS_1002368 search engine specific score for protein groups The probability based MaxQuant protein group score. http://purl.obolibrary.org/obo/MS_1003098 Andromeda peptide PEP http://purl.obolibrary.org/obo/MS_1002358 search engine specific peptide sequence-level identification statistic Peptide probability from Andromeda. http://purl.obolibrary.org/obo/MS_1003099 MaxQuant-DIA peptide PEP http://purl.obolibrary.org/obo/MS_1002358 search engine specific peptide sequence-level identification statistic Peptide probability from MaxQuant-DIA algorithm. http://purl.obolibrary.org/obo/MS_1003100 MaxQuant-DIA score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic PSM evidence score from MaxQuant-DIA algorithm. http://purl.obolibrary.org/obo/MS_1003101 MaxQuant-DIA PEP http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic PSM evidence PEP probability from MaxQuant-DIA algorithm. http://purl.obolibrary.org/obo/MS_1003102 NIST msp comment http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute Term for a comment field within the NIST msp file format http://purl.obolibrary.org/obo/MS_1003103 ion annotation format http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute Annotation format used for annotating individual spectrum ion peaks. http://purl.obolibrary.org/obo/MS_1003104 mzPAF peptide ion annotation format http://purl.obolibrary.org/obo/MS_1003103 ion annotation format Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions. http://purl.obolibrary.org/obo/MS_1003105 crosslinked peptide ion annotation format http://purl.obolibrary.org/obo/MS_1003103 ion annotation format Annotation format designed specifically for crosslinked peptide ion peaks. http://purl.obolibrary.org/obo/MS_1003106 glycan ion annotation format http://purl.obolibrary.org/obo/MS_1003103 ion annotation format Annotation format designed specifically for glycan ion peaks. http://purl.obolibrary.org/obo/MS_1003107 lipid ion annotation format http://purl.obolibrary.org/obo/MS_1003103 ion annotation format Annotation format designed specifically for lipid ion peaks. http://purl.obolibrary.org/obo/MS_1003108 PatternLab http://purl.obolibrary.org/obo/MS_1001456 analysis software PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data. http://purl.obolibrary.org/obo/MS_1003109 SIM-XL http://purl.obolibrary.org/obo/MS_1001456 analysis software Identifying crosslinked peptides in complex protein mixtures http://purl.obolibrary.org/obo/MS_1003110 SIM-XL score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic SIM-XL identification search engine score http://purl.obolibrary.org/obo/MS_1003111 QUIN-XL http://purl.obolibrary.org/obo/MS_1001139 quantitation software name Quantification of crosslinked peptides in complex protein mixtures http://purl.obolibrary.org/obo/MS_1003112 Orbitrap ID-X http://purl.obolibrary.org/obo/MS_1003770 quadrupole ion trap orbitrap instrument Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. http://purl.obolibrary.org/obo/MS_1003113 OpenMS:ConsensusID PEP http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The OpenMS ConsesusID tool posterior error probability http://purl.obolibrary.org/obo/MS_1003114 OpenMS:Best PSM Score http://purl.obolibrary.org/obo/MS_1002358 search engine specific peptide sequence-level identification statistic The score of the best PSM selected by the underlying identification tool http://purl.obolibrary.org/obo/MS_1003115 OpenMS:Target-decoy PSM q-value http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The OpenMS Target-decoy q-values at PSM level http://purl.obolibrary.org/obo/MS_1003116 OpenMS:Target-decoy peptide q-value http://purl.obolibrary.org/obo/MS_1002358 search engine specific peptide sequence-level identification statistic The OpenMS Target-decoy q-values at peptide sequence level http://purl.obolibrary.org/obo/MS_1003118 EPIFANY http://purl.obolibrary.org/obo/MS_1001456 analysis software A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework http://purl.obolibrary.org/obo/MS_1003119 EPIFANY:Protein posterior probability http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins Protein Posterior probability calculated by EPIFANY protein inference algorithm http://purl.obolibrary.org/obo/MS_1003120 OpenMS:LFQ intensity http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type LFQ intensity produced by OpenMS. http://purl.obolibrary.org/obo/MS_1003121 OpenMS:LFQ spectral count http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The data type LFQ spectral count produced by OpenMS. http://purl.obolibrary.org/obo/MS_1003122 rapifleX http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker Daltonics' rapiflex: MALDI TOF/TOF. http://purl.obolibrary.org/obo/MS_1003123 Bruker Daltonics timsTOF series http://purl.obolibrary.org/obo/MS_1000122 Bruker Daltonics instrument model Bruker Daltonics timsTOF series http://purl.obolibrary.org/obo/MS_1003124 timsTOF fleX http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker Daltonics' timsTOF fleX http://purl.obolibrary.org/obo/MS_1003136 ProSight input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to ProSight. http://purl.obolibrary.org/obo/MS_1003137 TDPortal input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to TDPortal. http://purl.obolibrary.org/obo/MS_1003138 ProSight:Run delta m mode http://purl.obolibrary.org/obo/MS_1003137 TDPortal input parameter If true, runs delta m mode in ProSight. http://purl.obolibrary.org/obo/MS_1003139 ProSight:Run Subsequence Search mode http://purl.obolibrary.org/obo/MS_1003137 TDPortal input parameter If true, runs Subsequence Search mode in ProSight. http://purl.obolibrary.org/obo/MS_1003140 ProSight:Run Annotated Proteoform Search mode http://purl.obolibrary.org/obo/MS_1003137 TDPortal input parameter If true, runs Annotated Proteoform Search mode in ProSight. http://purl.obolibrary.org/obo/MS_1003141 ProSight http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software ProSight: Database search engine for top-down proteomics. http://purl.obolibrary.org/obo/MS_1003142 TDPortal http://purl.obolibrary.org/obo/MS_1001456 analysis software TDPortal: Database search engine for top-down proteomics. http://purl.obolibrary.org/obo/MS_1003143 mass array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of mass values. http://purl.obolibrary.org/obo/MS_1003144 Triple Quad 7500 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX Triple Quad 7500. http://purl.obolibrary.org/obo/MS_1003145 ThermoRawFileParser http://purl.obolibrary.org/obo/MS_1001457 data processing software Cross-platform software to convert Thermo RAW files to a number of open formats. http://purl.obolibrary.org/obo/MS_1003146 pyteomics http://purl.obolibrary.org/obo/MS_1001456 analysis software Python module that helps handling various proteomics data analysis tasks. http://purl.obolibrary.org/obo/MS_1003147 PTMProphet probability http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet. http://purl.obolibrary.org/obo/MS_1003148 PTMProphet mean best probability http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet. http://purl.obolibrary.org/obo/MS_1003149 PTMProphet normalized information content http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic PTMProphet-computed PSM-specific normalized (0.0 - 1.0) measure of information content across all modifications of a specific type. http://purl.obolibrary.org/obo/MS_1003150 PTMProphet information content http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type. http://purl.obolibrary.org/obo/MS_1003151 SHA-256 http://purl.obolibrary.org/obo/MS_1000561 data file checksum type SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity. http://purl.obolibrary.org/obo/MS_1003152 GCMS-QP2010SE http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu Scientific Instruments GCMS-QP2010SE. http://purl.obolibrary.org/obo/MS_1003153 raw ion mobility drift time array http://purl.obolibrary.org/obo/MS_1002893 ion mobility array Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. http://purl.obolibrary.org/obo/MS_1003154 deconvoluted ion mobility array http://purl.obolibrary.org/obo/MS_1002893 ion mobility array Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. http://purl.obolibrary.org/obo/MS_1003155 deconvoluted inverse reduced ion mobility array http://purl.obolibrary.org/obo/MS_1002893 ion mobility array Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. http://purl.obolibrary.org/obo/MS_1003156 deconvoluted ion mobility drift time array http://purl.obolibrary.org/obo/MS_1002893 ion mobility array Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. http://purl.obolibrary.org/obo/MS_1003157 scanning quadrupole position lower bound m/z array http://purl.obolibrary.org/obo/MS_1000513 binary data array Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum. http://purl.obolibrary.org/obo/MS_1003158 scanning quadrupole position upper bound m/z array http://purl.obolibrary.org/obo/MS_1000513 binary data array Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum. http://purl.obolibrary.org/obo/MS_1003159 no isolation http://purl.obolibrary.org/obo/MS_1000792 isolation window attribute Indicates an acquisition mode in which the instrument does not perform isolation or where the window spans the entire mass range of the precursor spectrum. http://purl.obolibrary.org/obo/MS_1003160 mzQC format http://purl.obolibrary.org/obo/MS_1003161 quality control data format Proteomics Standards Initiative mzQC format for quality control data. http://purl.obolibrary.org/obo/MS_1003161 quality control data format http://purl.obolibrary.org/obo/MS_1001459 file format Grouping term for quality control data formats. http://purl.obolibrary.org/obo/MS_1003162 PTX-QC http://purl.obolibrary.org/obo/MS_1001456 analysis software Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization. http://purl.obolibrary.org/obo/MS_1003163 analyte mixture members http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute The set of analyte identifiers that compose an interpretation of a spectrum. http://purl.obolibrary.org/obo/MS_1003164 QuaMeter IDFree http://purl.obolibrary.org/obo/MS_1001456 analysis software QuaMeter IDFree software for QC metric calculation. http://purl.obolibrary.org/obo/MS_1003165 iMonDB http://purl.obolibrary.org/obo/MS_1001456 analysis software iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files. http://purl.obolibrary.org/obo/MS_1003166 assigned intensity fraction http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum http://purl.obolibrary.org/obo/MS_1003167 MSn-1 isolation window precursor purity http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte http://purl.obolibrary.org/obo/MS_1003168 library spectrum comment http://purl.obolibrary.org/obo/MS_1003234 library spectrum attribute A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools. http://purl.obolibrary.org/obo/MS_1003169 proforma peptidoform sequence http://purl.obolibrary.org/obo/MS_1000889 peptidoform sequence Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation http://purl.obolibrary.org/obo/MS_1003173 numeric attribute http://purl.obolibrary.org/obo/MS_1000547 object attribute An attribute that takes on a numeric value http://purl.obolibrary.org/obo/MS_1003181 combined dissociation method http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute Combination of two or more dissociation methods that are known by a special term. http://purl.obolibrary.org/obo/MS_1003182 electron-transfer/collision-induced dissociation http://purl.obolibrary.org/obo/MS_1003181 combined dissociation method Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID). http://purl.obolibrary.org/obo/MS_1003183 Synapt XS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters oa-ToF based Synapt XS. http://purl.obolibrary.org/obo/MS_1003184 SELECT SERIES Cyclic IMS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters oa-ToF based SELECT SERIES Cyclic IMS. http://purl.obolibrary.org/obo/MS_1003185 SELECT SERIES MRT http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters oa-ToF based SELECT SERIES MRT. http://purl.obolibrary.org/obo/MS_1003186 library format version http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Version number of the [PSI] library format specification http://purl.obolibrary.org/obo/MS_1003187 library identifier http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Short identifier for the library for easy reference, preferably but not necessarily globally unique http://purl.obolibrary.org/obo/MS_1003190 library version http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Version number of the library, usually referring to a certain release of a continually updated library http://purl.obolibrary.org/obo/MS_1003191 library URI http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute URI or URL that uniquely identifies the library http://purl.obolibrary.org/obo/MS_1003192 decoy spectrum http://purl.obolibrary.org/obo/MS_1003072 spectrum origin type A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching http://purl.obolibrary.org/obo/MS_1003193 shuffle-and-reposition decoy spectrum http://purl.obolibrary.org/obo/MS_1003192 decoy spectrum A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence. http://purl.obolibrary.org/obo/MS_1003194 precursor shift decoy spectrum http://purl.obolibrary.org/obo/MS_1003192 decoy spectrum A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum. http://purl.obolibrary.org/obo/MS_1003195 unnatural peptidoform decoy spectrum http://purl.obolibrary.org/obo/MS_1003192 decoy spectrum A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform http://purl.obolibrary.org/obo/MS_1003196 unrelated species decoy spectrum http://purl.obolibrary.org/obo/MS_1003192 decoy spectrum A decoy spectrum that is a real spectrum of a naturally occurring peptidoform of an unrelated species that should not be found in the sample http://purl.obolibrary.org/obo/MS_1003197 license URI http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/) http://purl.obolibrary.org/obo/MS_1003198 copyright notice http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work http://purl.obolibrary.org/obo/MS_1003199 change log http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Extended free-text description of the difference from the previous version http://purl.obolibrary.org/obo/MS_1003200 software version http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Version number of the software package used for library creation http://purl.obolibrary.org/obo/MS_1003201 library provenance attribute http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Abstract term containing several different types of provenance information http://purl.obolibrary.org/obo/MS_1003203 constituent spectrum file http://purl.obolibrary.org/obo/MS_1003201 library provenance attribute Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible. http://purl.obolibrary.org/obo/MS_1003204 constituent identification file http://purl.obolibrary.org/obo/MS_1003201 library provenance attribute Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible http://purl.obolibrary.org/obo/MS_1003205 constituent library file http://purl.obolibrary.org/obo/MS_1003201 library provenance attribute Source library URI which(at least) a subset of spectra were extracted from. http://purl.obolibrary.org/obo/MS_1003206 library creation log http://purl.obolibrary.org/obo/MS_1003201 library provenance attribute String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped http://purl.obolibrary.org/obo/MS_4000179 precursor ppm deviation sigma http://purl.obolibrary.org/obo/MS_4000003 single value The standard deviation of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied http://purl.obolibrary.org/obo/MS_1000660 Xevo MRT MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters Corporation Xevo MRT Mass Spectrometer. http://purl.obolibrary.org/obo/MS_1003424 selected fragment theoretical m/z observed intensity spectrum http://purl.obolibrary.org/obo/MS_1003072 spectrum origin type Spectrum for which the peaks are limited to a subset of known product ions that are important for subsequent identification, whose m/z values are corrected to theoretical values, and intensity values are experimentally derived. http://purl.obolibrary.org/obo/MS_1003425 quantms http://purl.obolibrary.org/obo/MS_1001456 analysis software Cloud-based pipeline for quantitative proteomics that enables the reanalysis of public proteomics data. http://purl.obolibrary.org/obo/MS_1003433 Andromeda:delta score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Score difference to the second best identified peptide with a different amino acid sequence. http://purl.obolibrary.org/obo/MS_4000182 XIC-Height quantile ratios http://purl.obolibrary.org/obo/MS_4000004 n-tuple The log ratio of successive XIC height quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of XIC-Height-Q2 to XIC-Height-Q1, XIC-Height-Q3 to XIC-Height-Q2, XIC-Height max to XIC-Height-Q3. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000183 TIC quantile RT fraction http://purl.obolibrary.org/obo/MS_4000004 n-tuple The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000184 MS1 quantile RT fraction http://purl.obolibrary.org/obo/MS_4000004 n-tuple The interval used for acquisition of quantiles of all MS1 events divided by retention time duration. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000185 MS2 quantile RT fraction http://purl.obolibrary.org/obo/MS_4000004 n-tuple The interval used for acquisition of quantiles of all MS2 events divided by retention time duration. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000186 MS1 TIC-change quantile ratios http://purl.obolibrary.org/obo/MS_4000004 n-tuple The log ratios of successive TIC-change quantiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. A value triplet represents the original QuaMeter metrics, the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000187 MS1 TIC quantile ratios http://purl.obolibrary.org/obo/MS_4000004 n-tuple The log ratios of successive TIC quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000188 identified MS2 quantile RT fraction http://purl.obolibrary.org/obo/MS_4000004 n-tuple The interval used for acquisition of quantiles of all identified MS2 events, after user-defined acceptance criteria are applied, divided by retention time duration. The number of values in the tuple implies the quantile mode. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. http://purl.obolibrary.org/obo/MS_1003905 targeted analysis http://purl.obolibrary.org/obo/MS_1003903 analysis An analytical approach in which a predefined set of analytes is measured, typically enabling quantitative determination. http://purl.obolibrary.org/obo/MS_1003971 ion trap fourier transform ion cyclotron resonance instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class An instrument that uses a linear ion trap coupled to a fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis. http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software http://purl.obolibrary.org/obo/MS_1000531 software Thermo Scientific software for data acquisition and analysis. http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class An instrument that uses an ion mobility analyzer followed by a quadrupole mass filter and a time-of-flight mass analyzer as its primary means of mass analysis. http://purl.obolibrary.org/obo/MS_1003972 quadrupole ion trap instrument http://purl.obolibrary.org/obo/MS_1003761 instrument class An instrument that uses a quadrupole mass filter followed by an ion trap mass analyzer as its primary means of mass analysis. http://purl.obolibrary.org/obo/MS_1003962 TraceFinder http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific software for targeted quantitative and screening analysis of LC-MS, GC-MS, and IC-MS data, supporting automated data acquisition, processing, and reporting for diverse workflows. http://purl.obolibrary.org/obo/MS_1003963 FreeStyle http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific software for interactive qualitative visualization and review of mass spectrometry data, including chromatographic peak detection, spectral library searching, and high-resolution deconvolution. http://purl.obolibrary.org/obo/MS_1003964 Chromeleon CDS http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific enterprise chromatography data system with integrated mass spectrometry instrument control and data processing, supporting GC-MS, LC-MS, and IC-MS platforms with GxP/21 CFR Part 11 compliance. http://purl.obolibrary.org/obo/MS_1003965 Mass Frontier http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific software for mass spectral interpretation and structural elucidation of small molecules, featuring the HighChem fragmentation library, fragmentation prediction, and spectral tree searching. http://purl.obolibrary.org/obo/MS_1003966 LipidSearch http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific software for automated identification of lipid molecular species from LC-MS and LC-MS/MS data using a comprehensive database of predicted lipid ion fragments. http://purl.obolibrary.org/obo/MS_1003967 mzVault http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific software for offline storage, searching, and management of high-resolution accurate-mass spectral libraries, including curated mzCloud content and user-generated in-house libraries. http://purl.obolibrary.org/obo/MS_1003968 SIEVE http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific software for label-free differential expression analysis of LC-MS and GC-MS data, providing chromatographic alignment, feature detection, and statistical comparison for proteomics and metabolomics. http://purl.obolibrary.org/obo/MS_1003969 BioPharma Finder http://purl.obolibrary.org/obo/MS_1003961 Thermo Scientific software Thermo Scientific software for complex biotherapeutic characterization by LC-MS, supporting intact protein analysis, peptide mapping, oligonucleotide analysis, multi-attribute method workflows, and top-down or middle-down approaches. http://purl.obolibrary.org/obo/UO_0000012 kelvin http://purl.obolibrary.org/obo/UO_0000045 base unit A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water. http://purl.obolibrary.org/obo/UO_0000028 millisecond http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to one thousandth of a second or 10^[-3] s. http://purl.obolibrary.org/obo/UO_0000045 base unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is one of a particular measure to which all measures of that type can be related. http://purl.obolibrary.org/obo/UO_0000052 mass density unit http://purl.obolibrary.org/obo/UO_0000182 density unit A density unit which is a standard measure of the mass of a substance in a given volume. http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. http://purl.obolibrary.org/obo/UO_0000187 percent http://purl.obolibrary.org/obo/UO_0000190 ratio A dimensionless ratio unit which denotes numbers as fractions of 100. http://purl.obolibrary.org/obo/UO_0000189 count unit http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit A dimensionless unit which denotes a simple count of things. http://purl.obolibrary.org/obo/MS_1002783 6550 iFunnel Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002784 6550A iFunnel Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002785 6520B Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002786 6530A Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002787 6530B Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002788 6538 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002789 6540 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002790 6542 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002791 6545 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002792 6560 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002793 6570 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002794 6120B Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. http://purl.obolibrary.org/obo/MS_1002795 6150 Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. http://purl.obolibrary.org/obo/MS_1002796 6224 Time-of-Flight LC/MS http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002797 6230A Time-of-Flight LC/MS http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002798 6230B Time-of-Flight LC/MS http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1002799 6430 Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002800 6495A Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002801 6495B Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002802 7000A Triple Quadrupole GC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002803 7000B Triple Quadrupole GC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002804 7800 Quadrupole ICP-MS http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002805 8800 Triple Quadrupole ICP-MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1002806 ion http://purl.obolibrary.org/obo/MS_1000881 molecular entity Molecular entity having a net positive or negative electric charge. http://purl.obolibrary.org/obo/MS_1002807 positive mode adduct ion http://purl.obolibrary.org/obo/MS_1000353 adduct ion Adduct ion with positive ionization. http://purl.obolibrary.org/obo/MS_1002808 negative mode adduct ion http://purl.obolibrary.org/obo/MS_1000353 adduct ion Adduct ion with negative ionization. http://purl.obolibrary.org/obo/MS_1002810 adduct ion X m/z http://purl.obolibrary.org/obo/MS_1003056 adduct ion property Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator. http://purl.obolibrary.org/obo/MS_1002811 adduct ion isotope http://purl.obolibrary.org/obo/MS_1003056 adduct ion property Isotope of the matrix molecule M of an adduct formation. http://purl.obolibrary.org/obo/MS_1002812 Regular expression for adduct ion formula http://purl.obolibrary.org/obo/MS_1002479 regular expression ([[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}][:digit:]{0,1}[+-]). http://purl.obolibrary.org/obo/MS_1002813 adduct ion formula http://purl.obolibrary.org/obo/MS_1002809 adduct ion attribute Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression. http://purl.obolibrary.org/obo/MS_1002814 volt-second per square centimeter http://purl.obolibrary.org/obo/UO_0000000 unit An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]. http://purl.obolibrary.org/obo/MS_1002815 inverse reduced ion mobility http://purl.obolibrary.org/obo/MS_1003254 peak attribute Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated. http://purl.obolibrary.org/obo/MS_1002816 mean ion mobility array http://purl.obolibrary.org/obo/MS_1002893 ion mobility array Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. http://purl.obolibrary.org/obo/MS_1002817 Bruker TDF format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Bruker TDF raw file format. http://purl.obolibrary.org/obo/MS_1002818 Bruker TDF nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1002819 Bruker TDF nativeID format, combined spectra http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation. http://purl.obolibrary.org/obo/MS_1002820 M+H ion http://purl.obolibrary.org/obo/MS_1002807 positive mode adduct ion Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton. http://purl.obolibrary.org/obo/MS_1002821 M-H ion http://purl.obolibrary.org/obo/MS_1002808 negative mode adduct ion Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M. http://purl.obolibrary.org/obo/MS_1002885 standard error http://purl.obolibrary.org/obo/MS_1002884 study variable variation function Standard error function. http://purl.obolibrary.org/obo/MS_1003034 atom http://purl.obolibrary.org/obo/MS_1000881 molecular entity Smallest constituent unit of ordinary matter that constitutes a chemical element. http://purl.obolibrary.org/obo/MS_1003035 small molecule http://purl.obolibrary.org/obo/MS_1000859 molecule Low molecular weight (< 900 daltons) organic compound that may regulate a biological process. http://purl.obolibrary.org/obo/MS_1003036 metabolite http://purl.obolibrary.org/obo/MS_1003035 small molecule Small molecule that is the intermediate end product of metabolism. http://purl.obolibrary.org/obo/MS_1003037 ribonucleotide http://purl.obolibrary.org/obo/MS_1003035 small molecule Nucleotide containing ribose as its pentose component. http://purl.obolibrary.org/obo/MS_1003038 deoxyribonucleotide http://purl.obolibrary.org/obo/MS_1003035 small molecule Monomer, or single unit, of DNA, or deoxyribonucleic acid. http://purl.obolibrary.org/obo/MS_1003039 amino acid http://purl.obolibrary.org/obo/MS_1003035 small molecule Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid. http://purl.obolibrary.org/obo/MS_1003040 monosaccharide http://purl.obolibrary.org/obo/MS_1003035 small molecule Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule. http://purl.obolibrary.org/obo/MS_1003041 nucleic acid http://purl.obolibrary.org/obo/MS_1000859 molecule Molecule composed of a chain of nucleotides. http://purl.obolibrary.org/obo/MS_1003042 polysaccharide http://purl.obolibrary.org/obo/MS_1000859 molecule Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages. http://purl.obolibrary.org/obo/MS_1003043 number of residues http://purl.obolibrary.org/obo/MS_1000887 peptide attribute Number of amino acid residues in a peptide, commonly referred to as the peptide length. http://purl.obolibrary.org/obo/MS_1003044 number of missed cleavages http://purl.obolibrary.org/obo/MS_1000887 peptide attribute Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not. http://purl.obolibrary.org/obo/MS_1003045 peptide-to-protein mapping http://purl.obolibrary.org/obo/MS_1000887 peptide attribute Process of mapping a peptide sequence to a protein sequence. http://purl.obolibrary.org/obo/MS_1003046 peptide-to-protein mapping attribute http://purl.obolibrary.org/obo/MS_1003045 peptide-to-protein mapping Nonphysical characteristic attributed to the result of peptide-to-protein mapping. http://purl.obolibrary.org/obo/MS_1003047 protein sequence offset http://purl.obolibrary.org/obo/MS_1003046 peptide-to-protein mapping attribute Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence. http://purl.obolibrary.org/obo/MS_1003048 number of enzymatic termini http://purl.obolibrary.org/obo/MS_1003046 peptide-to-protein mapping attribute Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules. http://purl.obolibrary.org/obo/MS_1003049 peptidoform http://purl.obolibrary.org/obo/MS_1000860 peptide Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations. http://purl.obolibrary.org/obo/MS_1003051 peptidoform ion http://purl.obolibrary.org/obo/MS_1003049 peptidoform Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'. http://purl.obolibrary.org/obo/MS_1003053 theoretical monoisotopic m/z http://purl.obolibrary.org/obo/MS_1003052 peptidoform ion property Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents. http://purl.obolibrary.org/obo/MS_1003054 theoretical average m/z http://purl.obolibrary.org/obo/MS_1003052 peptidoform ion property Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes. http://purl.obolibrary.org/obo/MS_1003055 adduct http://purl.obolibrary.org/obo/MS_1000859 molecule Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species. http://purl.obolibrary.org/obo/MS_1003057 scan number http://purl.obolibrary.org/obo/MS_1000503 scan attribute Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run. http://purl.obolibrary.org/obo/MS_1003059 number of peaks http://purl.obolibrary.org/obo/MS_1003058 spectrum property Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernible in the spectrum, which will be fewer than the number of data points. http://purl.obolibrary.org/obo/MS_1003060 number of data points http://purl.obolibrary.org/obo/MS_1003058 spectrum property Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks. http://purl.obolibrary.org/obo/MS_1003061 library spectrum name http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection. http://purl.obolibrary.org/obo/MS_1003062 library spectrum index http://purl.obolibrary.org/obo/MS_1003234 library spectrum attribute Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0. http://purl.obolibrary.org/obo/MS_1003063 universal spectrum identifier http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library. http://purl.obolibrary.org/obo/MS_1003064 spectrum aggregation attribute http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute Non-inherent characteristic attributed to spectrum aggregation. http://purl.obolibrary.org/obo/MS_1003065 spectrum aggregation type http://purl.obolibrary.org/obo/MS_1003064 spectrum aggregation attribute Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.). http://purl.obolibrary.org/obo/MS_1003066 singleton spectrum http://purl.obolibrary.org/obo/MS_1003065 spectrum aggregation type Spectrum that is not the result of some aggregation process. http://purl.obolibrary.org/obo/MS_1003067 consensus spectrum http://purl.obolibrary.org/obo/MS_1003065 spectrum aggregation type Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates. http://purl.obolibrary.org/obo/MS_1003068 best replicate spectrum http://purl.obolibrary.org/obo/MS_1003065 spectrum aggregation type Spectrum that is considered the most representative from a pool of replicate spectra. http://purl.obolibrary.org/obo/MS_1003069 number of replicate spectra available http://purl.obolibrary.org/obo/MS_1003064 spectrum aggregation attribute Number of replicate spectra available for use during the aggregation process. http://purl.obolibrary.org/obo/MS_1003070 number of replicate spectra used http://purl.obolibrary.org/obo/MS_1003064 spectrum aggregation attribute Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm. http://purl.obolibrary.org/obo/MS_1003071 spectrum origin attribute http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute Non-inherent characteristic attributed to spectrum aggregation. http://purl.obolibrary.org/obo/MS_1003072 spectrum origin type http://purl.obolibrary.org/obo/MS_1003071 spectrum origin attribute Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.). http://purl.obolibrary.org/obo/MS_1003073 observed spectrum http://purl.obolibrary.org/obo/MS_1003072 spectrum origin type Spectrum that originates from an analysis attempt of a single analyte species on an instrument. http://purl.obolibrary.org/obo/MS_1003074 predicted spectrum http://purl.obolibrary.org/obo/MS_1003072 spectrum origin type Spectrum that originates from a compututational algorithm that attempts to predict spectra. http://purl.obolibrary.org/obo/MS_1003075 demultiplexed spectrum http://purl.obolibrary.org/obo/MS_1003072 spectrum origin type Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species. http://purl.obolibrary.org/obo/MS_1003076 uninterpreted spectrum http://purl.obolibrary.org/obo/MS_1000442 spectrum Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features. http://purl.obolibrary.org/obo/MS_1003077 interpreted spectrum http://purl.obolibrary.org/obo/MS_1000442 spectrum Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature. http://purl.obolibrary.org/obo/MS_1003079 total unassigned intensity fraction http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum. http://purl.obolibrary.org/obo/MS_1003080 top 20 peak unassigned intensity fraction http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum. http://purl.obolibrary.org/obo/MS_1003081 unidentified modification monoisotopic mass delta http://purl.obolibrary.org/obo/MS_1001471 peptide modification details Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the element in mzIdentML. http://purl.obolibrary.org/obo/MS_1003082 MS-DIAL http://purl.obolibrary.org/obo/MS_1002878 small molecule analysis software Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors. http://purl.obolibrary.org/obo/MS_1003437 lowest observed ion mobility http://purl.obolibrary.org/obo/MS_1003058 spectrum property Lowest ion mobility value observed in the ion mobility measurement array. http://purl.obolibrary.org/obo/MS_1003438 highest observed ion mobility http://purl.obolibrary.org/obo/MS_1003058 spectrum property Highest ion mobility value observed in the ion mobility measurement array. http://purl.obolibrary.org/obo/MS_1003439 ion mobility frame representation http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute Representation of one or more spectra acquired across an ion mobility dimension. http://purl.obolibrary.org/obo/MS_1003440 ion mobility profile frame http://purl.obolibrary.org/obo/MS_1003439 ion mobility frame representation An ion mobility frame where the ion mobility dimension is continuous. http://purl.obolibrary.org/obo/MS_1003441 ion mobility centroid frame http://purl.obolibrary.org/obo/MS_1003439 ion mobility frame representation An ion mobility frame where the ion mobility dimension is processed into discrete peaks of zero width. http://purl.obolibrary.org/obo/MS_1003509 Synapt G2-Si HDMS http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters Synapt G2-Si HDMS quadrupole - ion mobility - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003515 5973N MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5973N MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003800 TSQ Certis http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Scientific TSQ Certis Triple Quadrupole MS. http://purl.obolibrary.org/obo/MS_1002961 isotopologue http://purl.obolibrary.org/obo/MS_1002959 isomer A molecular entity that differs only in isotopic composition (number of isotopic substitutions). http://purl.obolibrary.org/obo/MS_1002919 TopPIC:spectral cutoff type http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Spectrum-level cutoff type for filtering identified proteoform spectrum matches. http://purl.obolibrary.org/obo/MS_1000394 no sequence database http://purl.obolibrary.org/obo/MS_1001347 database file formats No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing. http://purl.obolibrary.org/obo/MS_1002866 Reference http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet. http://purl.obolibrary.org/obo/MS_1002863 Data derived from previous dataset http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter One dataset is a reanalysis of previously published data. http://purl.obolibrary.org/obo/MS_1002850 Peak list file URI http://purl.obolibrary.org/obo/MS_1002845 Associated file URI URI of one of one search engine output file associated to one PX submission. http://purl.obolibrary.org/obo/MS_1002849 Search engine output file URI http://purl.obolibrary.org/obo/MS_1002845 Associated file URI URI of one search engine output file associated to one PX submission. http://purl.obolibrary.org/obo/MS_1002864 No PTMs are included in the dataset http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter No post-translational-modifications are been included in the identified peptides of one dataset. http://purl.obolibrary.org/obo/MS_1002960 isotopomer http://purl.obolibrary.org/obo/MS_1002959 isomer An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms. http://purl.obolibrary.org/obo/MS_1002955 hr-ms compound identification confidence level http://purl.obolibrary.org/obo/MS_1002895 small molecule identification attribute Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'. http://purl.obolibrary.org/obo/MS_1002956 isotopic ion MS peak http://purl.obolibrary.org/obo/MS_1000231 peak A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'. http://purl.obolibrary.org/obo/MS_1002908 proteoform-level local FDR http://purl.obolibrary.org/obo/MS_1002905 proteoform-level identification statistic Estimation of the local false discovery rate of proteoforms. http://purl.obolibrary.org/obo/MS_1003028 Orbitrap Exploris 480 http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS. http://purl.obolibrary.org/obo/MS_1003029 Orbitrap Eclipse http://purl.obolibrary.org/obo/MS_1003770 quadrupole ion trap orbitrap instrument Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. http://purl.obolibrary.org/obo/MS_1003127 ProSight:spectral E-value http://purl.obolibrary.org/obo/MS_1002353 PSM-level e-value ProSight spectrum-level E-value. http://purl.obolibrary.org/obo/MS_1003426 xQuest/xProphet http://purl.obolibrary.org/obo/MS_1001456 analysis software A software to identify cross-linked peptides from LC-MS/MS spectra. http://purl.obolibrary.org/obo/MS_1003427 PeakView http://purl.obolibrary.org/obo/MS_1001456 analysis software A software for spectral analysis and data interrogation in qualitative review of LC-MS and MS/MS data. http://purl.obolibrary.org/obo/MS_1003428 Perseus http://purl.obolibrary.org/obo/MS_1001456 analysis software A software for interpreting protein quantification, interaction and post-translational modification data. http://purl.obolibrary.org/obo/MS_1003429 FragPipe http://purl.obolibrary.org/obo/MS_1001456 analysis software A computational platform for analyzing mass spectrometry-based proteomics data. http://purl.obolibrary.org/obo/MS_1003430 OpenMS http://purl.obolibrary.org/obo/MS_1001456 analysis software A software for LC-MS data management and analysis. http://purl.obolibrary.org/obo/MS_1003431 pLink http://purl.obolibrary.org/obo/MS_1001456 analysis software A tool for the analysis of chemically cross-linked proteins using mass spectrometry. http://purl.obolibrary.org/obo/MS_1003432 pLink2 http://purl.obolibrary.org/obo/MS_1003431 pLink Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure. http://purl.obolibrary.org/obo/NCIT_C68811 Cover http://purl.obolibrary.org/obo/NCIT_C25404 Action Span a region or interval of distance, space or time. http://purl.obolibrary.org/obo/NCIT_C79083 Outlier http://purl.obolibrary.org/obo/NCIT_C20181 Conceptual Entity An observation in a data set that is numerically distant from the rest of the data. http://purl.obolibrary.org/obo/MS_1002832 XCMS:area http://purl.obolibrary.org/obo/MS_1002735 feature-level quantification datatype Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate. http://purl.obolibrary.org/obo/MS_1002869 mzR http://purl.obolibrary.org/obo/MS_1001457 data processing software Bioconductor package mzR for reading and writing mass spectrometry data files. http://purl.obolibrary.org/obo/MS_1002870 MSnbase http://purl.obolibrary.org/obo/MS_1001457 data processing software Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. http://purl.obolibrary.org/obo/MS_1002871 CAMERA http://purl.obolibrary.org/obo/MS_1001457 data processing software Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments. http://purl.obolibrary.org/obo/MS_1002907 proteoform-level global FDR http://purl.obolibrary.org/obo/MS_1002905 proteoform-level identification statistic Estimation of the global false discovery rate of proteoforms. http://purl.obolibrary.org/obo/NCIT_C150827 Number of Occurrences http://purl.obolibrary.org/obo/NCIT_C25337 Number The number of times something happened. http://purl.obolibrary.org/obo/MS_1003397 timsTOF fleX MALDI-2 http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker Daltonics' timsTOF fleX MALDI-2. http://purl.obolibrary.org/obo/MS_1003395 Q Exactive GC Orbitrap http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003413 Kojak http://purl.obolibrary.org/obo/MS_1001456 analysis software Kojak open-source crosslinked peptide sequence search engine developed at the Institute for Systems Biology. http://purl.obolibrary.org/obo/MS_1003414 Kojak:score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Kojak score for an individual peptide sequence, similar to Comet:xcorr. http://purl.obolibrary.org/obo/MS_1003415 Kojak:expectation value http://purl.obolibrary.org/obo/MS_1001153 search engine specific score The Kojak expectation value for an individual peptide sequence. http://purl.obolibrary.org/obo/MS_1003416 Kojak:matched ions http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The number of matched ions for an individual peptide sequence in a Kojak result. http://purl.obolibrary.org/obo/MS_1003417 Kojak:consecutive matched ions http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The highest run of consecutive matched ions for an individual peptide sequence in a Kojak result. http://purl.obolibrary.org/obo/MS_1003418 Kojak:delta score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The difference between the top Kojak score and the next best Kojak score for a PSM. http://purl.obolibrary.org/obo/MS_1003419 Kojak:rank http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The rank of an individual peptide from the first pass of the Kojak scoring algorithm. Applies only to sequences in a crosslinked result. http://purl.obolibrary.org/obo/MS_1003420 Kojak:score xlink http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The Kojak score for a crosslinked pair of peptide sequences, similar to Comet:xcorr. http://purl.obolibrary.org/obo/MS_1003421 Kojak:expectation value xlink http://purl.obolibrary.org/obo/MS_1001153 search engine specific score The Kojak expectation value for a crosslinked pair of peptide sequences. http://purl.obolibrary.org/obo/MS_1003422 Kojak:matched ions xlink http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic The number of matched ions for a crosslinked pair of peptide sequences in a Kojak result. http://purl.obolibrary.org/obo/MS_1001185 Mobilion MBI format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Mobilion MBI file format. http://purl.obolibrary.org/obo/MS_1001186 Mobilion MBI nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1002992 Orbitrap Exploris GC-MS http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Orbitrap Exploris GC-MS. http://purl.obolibrary.org/obo/MS_1003457 Triple Quad 5500+ http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX Triple Quad 5500+ triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/NCIT_C25337 Number http://purl.obolibrary.org/obo/NCIT_C20189 Property or Attribute A numeral or string of numerals expressing value, quantity, or identification. http://purl.obolibrary.org/obo/NCIT_C25404 Action http://purl.obolibrary.org/obo/NCIT_C43431 Activity A thing done. http://purl.obolibrary.org/obo/NCIT_C16847 Technique http://purl.obolibrary.org/obo/NCIT_C43431 Activity A practiced and regimented skill or series of actions. http://purl.obolibrary.org/obo/MS_1002995 Andromeda:PEP http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic Posterior error probability of the best identified peptide of the Andromeda search engine. http://purl.obolibrary.org/obo/MS_1003031 CPTAC accession number http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Main identifier of a CPTAC dataset. http://purl.obolibrary.org/obo/MS_1003188 library name http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library. http://purl.obolibrary.org/obo/MS_1003235 paper spray ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type The ionization of analytes from a piece of paper by applying a solvent and voltage. http://purl.obolibrary.org/obo/MS_4000180 table of missed cleavage counts http://purl.obolibrary.org/obo/MS_4000005 table The number of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective count of such peptides identified in the 'Number of Occurrences' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher. http://purl.obolibrary.org/obo/MS_1003396 8890 http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model Agilent 8890 gas chromatograph. http://purl.obolibrary.org/obo/MS_1003904 untargeted analysis http://purl.obolibrary.org/obo/MS_1003903 analysis An analytical approach in which comprehensive detection of all measurable analytes is attempted without prior specification of target compounds. http://purl.obolibrary.org/obo/MS_1003906 semi-targeted analysis http://purl.obolibrary.org/obo/MS_1003903 analysis An analytical approach combining targeted monitoring of predefined analytes with simultaneous untargeted data acquisition. http://purl.obolibrary.org/obo/MS_1003907 parallel reaction monitoring http://purl.obolibrary.org/obo/MS_1003214 mass spectrometry acquisition method aspect Parallel Reaction Monitoring (PRM) utilizes high-resolution, accurate-mass mass spectrometry, typically a quadrupole orbitrap or quadrupole time-of-flight instrument, to isolate specific precursor ions and detect all resulting product ions in parallel. Unlike Selected Reaction Monitoring (SRM), which filters for pre-selected transitions, PRM acquires full MS/MS spectra for each target, thereby eliminating the need for transition optimization and providing high specificity through high-resolution interference rejection. http://purl.obolibrary.org/obo/MS_1000073 electrospray ionization http://purl.obolibrary.org/obo/MS_1000008 ionization type A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended. http://purl.obolibrary.org/obo/MS_1002742 noise array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of noise values. http://purl.obolibrary.org/obo/MS_1002743 sampled noise m/z array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array). http://purl.obolibrary.org/obo/MS_1002744 sampled noise intensity array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array). http://purl.obolibrary.org/obo/MS_1002745 sampled noise baseline array http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array). http://purl.obolibrary.org/obo/MS_1002746 MS-Numpress linear prediction compression followed by zlib compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression using MS-Numpress linear prediction compression and zlib. http://purl.obolibrary.org/obo/MS_1002747 MS-Numpress positive integer compression followed by zlib compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression using MS-Numpress positive integer compression and zlib. http://purl.obolibrary.org/obo/MS_1002748 MS-Numpress short logged float compression followed by zlib compression http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression using MS-Numpress short logged float compression and zlib. http://purl.obolibrary.org/obo/MS_1002749 Mascot:IntegratedSpectralLibrarySearch http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter Means that Mascot has integrated the search results of database and spectral library search into a single data set. http://purl.obolibrary.org/obo/MS_1002750 NIST MSPepSearch http://purl.obolibrary.org/obo/MS_1001456 analysis software Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches. http://purl.obolibrary.org/obo/MS_1002751 NIST MSP format http://purl.obolibrary.org/obo/MS_1001347 database file formats MSP text format defined by the NIST. http://purl.obolibrary.org/obo/MS_1002752 database type spectral library http://purl.obolibrary.org/obo/MS_1001073 database type amino acid Database containing spectra. http://purl.obolibrary.org/obo/MS_1002753 value between 0 and 1000 inclusive http://purl.obolibrary.org/obo/MS_1002304 domain range Value range for scores. http://purl.obolibrary.org/obo/MS_1002754 MSPepSearch:score http://purl.obolibrary.org/obo/MS_1001143 PSM-level search engine specific statistic MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum. http://purl.obolibrary.org/obo/MS_1002755 combined ms-ms + spectral library search http://purl.obolibrary.org/obo/MS_1001080 search type A combined MS2 (with fragment ions) and spectral library search. http://purl.obolibrary.org/obo/NCIT_C25447 Characteristic http://purl.obolibrary.org/obo/NCIT_C20189 Property or Attribute The distinguishing qualities or prominent aspect of a person, object, action, process, or substance. http://purl.obolibrary.org/obo/NCIT_C19044 Statistical Technique http://purl.obolibrary.org/obo/NCIT_C16847 Technique A method of analyzing or representing statistical data; a procedure for calculating a statistic. http://purl.obolibrary.org/obo/MS_1002997 ProteomeXchange dataset identifier reanalysis number http://purl.obolibrary.org/obo/MS_1000878 external reference identifier Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD). http://purl.obolibrary.org/obo/MS_1003093 Lys-N http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues. http://purl.obolibrary.org/obo/MS_1000830 precision http://purl.obolibrary.org/obo/MS_1000480 mass analyzer attribute Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation. http://purl.obolibrary.org/obo/MS_1003407 Scout http://purl.obolibrary.org/obo/MS_1001456 analysis software Identifying crosslinked peptides in complex protein mixtures http://purl.obolibrary.org/obo/MS_1003411 Orbitrap IQ-X http://purl.obolibrary.org/obo/MS_1003770 quadrupole ion trap orbitrap instrument Thermo Scientific Orbitrap IQ-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. http://purl.obolibrary.org/obo/MS_1003412 timsTOF Ultra 2 http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker Daltonics timsTOF Ultra 2. http://purl.obolibrary.org/obo/MS_1002717 Waters DATA Convert http://purl.obolibrary.org/obo/MS_1001457 data processing software Software for processing and exporting Waters MassLynx and waters_connect data. http://purl.obolibrary.org/obo/MS_1003446 SCIEX OS http://purl.obolibrary.org/obo/MS_1001457 data processing software SCIEX OS software. http://purl.obolibrary.org/obo/MS_1003776 acquisition polarity http://purl.obolibrary.org/obo/MS_1000524 data file content The ion polarity configuration used during data acquisition of a sample run. http://purl.obolibrary.org/obo/MS_1003915 two-dimensional gas chromatography http://purl.obolibrary.org/obo/MS_1002272 gas chromatography separation Comprehensive two-dimensional gas chromatography (GCxGC) is a multidimensional separation technique that utilizes two columns with different stationary phases connected by a modulator, which traps, focuses and reinjects fractions from the first column to the second. This approach leads to a 2D chromatogram offering higher peak capacity and separation power. http://purl.obolibrary.org/obo/MS_1002838 mzMLb format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format mzMLb file format, mzML encapsulated within HDF5. http://purl.obolibrary.org/obo/MS_1002839 Conversion to mzMLb http://purl.obolibrary.org/obo/MS_1000530 file format conversion Conversion of a file format to Proteomics Standards Initiative mzMLb file format. http://purl.obolibrary.org/obo/MS_1002841 external HDF5 dataset http://purl.obolibrary.org/obo/MS_1002840 external reference data The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the section of the BinaryDataArray. http://purl.obolibrary.org/obo/MS_1002842 external offset http://purl.obolibrary.org/obo/MS_1002840 external reference data The position in the external data where the array begins. http://purl.obolibrary.org/obo/MS_1002843 external array length http://purl.obolibrary.org/obo/MS_1002840 external reference data Describes how many fields an array contains. http://purl.obolibrary.org/obo/MS_1002951 TopMG:spectral FDR http://purl.obolibrary.org/obo/MS_1002351 PSM-level local FDR TopMG spectrum-level FDR. http://purl.obolibrary.org/obo/MS_1002878 small molecule analysis software http://purl.obolibrary.org/obo/MS_1001456 analysis software Software for the analysis of small molecules. http://purl.obolibrary.org/obo/MS_1002880 Compound Discoverer http://purl.obolibrary.org/obo/MS_1002878 small molecule analysis software Metabolomics analysis software from Thermo Fisher Scientific. http://purl.obolibrary.org/obo/MS_1002881 MyCompoundID http://purl.obolibrary.org/obo/MS_1002878 small molecule analysis software Metabolite identification tool MyCompoundID. http://purl.obolibrary.org/obo/MS_1002882 study variable average function http://purl.obolibrary.org/obo/MS_1001184 search statistics Function used to calculate the study variable quantification value. http://purl.obolibrary.org/obo/MS_1002883 median http://purl.obolibrary.org/obo/MS_1002882 study variable average function Median function. http://purl.obolibrary.org/obo/MS_1002884 study variable variation function http://purl.obolibrary.org/obo/MS_1001184 search statistics Function used to calculate the study variable quantification variation value. http://purl.obolibrary.org/obo/MS_1002886 small molecule quantification datatype http://purl.obolibrary.org/obo/MS_1001805 quantification datatype The value reported in a small molecule quantification. http://purl.obolibrary.org/obo/MS_1002887 Progenesis QI normalised abundance http://purl.obolibrary.org/obo/MS_1002886 small molecule quantification datatype The normalised abundance produced by Progenesis QI LC-MS. http://purl.obolibrary.org/obo/MS_1002888 small molecule confidence measure http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute The confidence score produced by a small molecule analysis software. http://purl.obolibrary.org/obo/MS_1002889 Progenesis MetaScope score http://purl.obolibrary.org/obo/MS_1002888 small molecule confidence measure The confidence score produced by Progenesis QI. http://purl.obolibrary.org/obo/MS_1002890 fragmentation score http://purl.obolibrary.org/obo/MS_1002888 small molecule confidence measure The fragmentation confidence score. http://purl.obolibrary.org/obo/MS_1002891 isotopic fit score http://purl.obolibrary.org/obo/MS_1002888 small molecule confidence measure The isotopic fit confidence score. http://purl.obolibrary.org/obo/MS_1002892 ion mobility attribute http://purl.obolibrary.org/obo/MS_1002345 PSM-level attribute An attribute describing ion mobility searches. http://purl.obolibrary.org/obo/MS_1002893 ion mobility array http://purl.obolibrary.org/obo/MS_1000513 binary data array Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided. http://purl.obolibrary.org/obo/MS_1002899 msalign format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format msalign file format. http://purl.obolibrary.org/obo/MS_1002901 TopPIC http://purl.obolibrary.org/obo/MS_1001456 analysis software TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. http://purl.obolibrary.org/obo/MS_1002902 TopFD http://purl.obolibrary.org/obo/MS_1001456 analysis software Top-down mass spectral feature detection. http://purl.obolibrary.org/obo/MS_1002903 TopMG http://purl.obolibrary.org/obo/MS_1001456 analysis software A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra. http://purl.obolibrary.org/obo/MS_1002905 proteoform-level identification statistic http://purl.obolibrary.org/obo/MS_1002904 proteoform-level identification attribute Identification confidence metric for a proteoform. http://purl.obolibrary.org/obo/MS_1002906 search engine specific score for proteoforms http://purl.obolibrary.org/obo/MS_1002905 proteoform-level identification statistic Search engine specific proteoform scores. http://purl.obolibrary.org/obo/MS_1002909 proteoform-level statistical threshold http://purl.obolibrary.org/obo/MS_1002573 spectrum identification statistical threshold Estimated statistical threshold at proteoform-level. http://purl.obolibrary.org/obo/MS_1002910 proteoform-level global FDR threshold http://purl.obolibrary.org/obo/MS_1002909 proteoform-level statistical threshold Threshold for the global false discovery rate of proteoforms. http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to TopPIC. http://purl.obolibrary.org/obo/MS_1002916 TopPIC:max shift http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Maximum value of the mass shift (in Dalton) of an unexpected modification. http://purl.obolibrary.org/obo/MS_1002917 TopPIC:min shift http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Minimum value of the mass shift (in Dalton) of an unexpected modification. http://purl.obolibrary.org/obo/MS_1002918 TopPIC:shift num http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Maximum number of unexpected modifications in a proteoform spectrum match. http://purl.obolibrary.org/obo/MS_1002920 TopPIC:spectral cutoff value http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Spectrum-level cutoff value for filtering identified proteoform spectrum matches. http://purl.obolibrary.org/obo/MS_1002921 TopPIC:proteoform-level cutoff type http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Proteoform-level cutoff type for filtering identified proteoform spectrum matches. http://purl.obolibrary.org/obo/MS_1002923 TopPIC:generating function http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter P-value and E-value estimation using generating function. http://purl.obolibrary.org/obo/MS_1002925 TopPIC:mod file http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter The text file containing the information of common PTMs. http://purl.obolibrary.org/obo/MS_1002927 TopPIC:use TopFD feature http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Proteoform identification using TopFD feature file. http://purl.obolibrary.org/obo/MS_1002928 TopPIC:spectral E-value http://purl.obolibrary.org/obo/MS_1002353 PSM-level e-value TopPIC spectrum-level E-value. http://purl.obolibrary.org/obo/MS_1002929 TopPIC:spectral FDR http://purl.obolibrary.org/obo/MS_1002351 PSM-level local FDR TopPIC spectrum-level FDR. http://purl.obolibrary.org/obo/MS_1002931 TopPIC:spectral p-value http://purl.obolibrary.org/obo/MS_1002352 PSM-level p-value TopPIC spectrum-level p-value. http://purl.obolibrary.org/obo/MS_1002932 TopPIC:MIScore http://purl.obolibrary.org/obo/MS_1001968 PTM localization PSM-level statistic Modification identification score. http://purl.obolibrary.org/obo/MS_1002933 TopPIC:MIScore threshold http://purl.obolibrary.org/obo/MS_1002555 PTM localization score threshold TopPIC:MIScore threshold. http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter http://purl.obolibrary.org/obo/MS_1001302 search engine specific input parameter Search engine input parameters specific to TopMG. http://purl.obolibrary.org/obo/MS_1002936 TopMG:N-term form http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter N-terminal forms of proteins allowed in TopMG searching. http://purl.obolibrary.org/obo/MS_1002937 TopMG:error tolerance http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Error tolerance for precursor and fragment masses in PPM. http://purl.obolibrary.org/obo/MS_1002938 TopMG:max shift http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Maximum value of the mass shift (in Dalton). http://purl.obolibrary.org/obo/MS_1002941 TopMG:proteoform-level cutoff type http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Proteoform-level cutoff type for filtering identified proteoform spectrum matches. http://purl.obolibrary.org/obo/MS_1002942 TopMG:proteoform-level cutoff value http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Proteoform-level cutoff value for filtering identified proteoform spectrum matches. http://purl.obolibrary.org/obo/MS_1002943 TopMG:mod file http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter The text file containing the information of common PTMs. http://purl.obolibrary.org/obo/MS_1002944 TopMG:thread number http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Number of threads used in TopMG. http://purl.obolibrary.org/obo/MS_1002945 TopMG:use TopFD feature http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Proteoform identification using TopFD feature file. http://purl.obolibrary.org/obo/MS_1002946 TopMG:proteoform graph gap size http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Gap size in constructing proteoform graph. http://purl.obolibrary.org/obo/MS_1002947 TopMG:variable PTM number http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Maximum number of variable PTMs. http://purl.obolibrary.org/obo/MS_1002948 TopMG:variable PTM number in proteoform graph gap http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Maximum number of variable PTMs in a proteoform graph gap. http://purl.obolibrary.org/obo/MS_1002949 TopMG:use ASF-DIAGONAL http://purl.obolibrary.org/obo/MS_1002934 TopMG input parameter Protein filtering using ASF-DIAGONAL method. http://purl.obolibrary.org/obo/MS_1002950 TopMG:spectral E-value http://purl.obolibrary.org/obo/MS_1002353 PSM-level e-value TopMG spectrum-level E-value. http://purl.obolibrary.org/obo/MS_1002952 TopMG:proteoform-level FDR http://purl.obolibrary.org/obo/MS_1002906 search engine specific score for proteoforms TopMG proteoform-level FDR. http://purl.obolibrary.org/obo/MS_1002962 mean http://purl.obolibrary.org/obo/MS_1002882 study variable average function The arithmetic mean. http://purl.obolibrary.org/obo/MS_1002963 variation coefficient http://purl.obolibrary.org/obo/MS_1002884 study variable variation function The coefficient of variation. http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software http://purl.obolibrary.org/obo/MS_1002878 small molecule analysis software Lipidomics analysis software. http://purl.obolibrary.org/obo/MS_1002965 Lipid Data Analyzer http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Lipid Data Analyzer software for lipid quantification. http://purl.obolibrary.org/obo/MS_1002966 chrom format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format The Lipid Data Analyzer native chrom format. http://purl.obolibrary.org/obo/MS_1002967 LipidHunter http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets. http://purl.obolibrary.org/obo/MS_1002968 LipidXplorer http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Software for consensual cross-platform lipidomics. http://purl.obolibrary.org/obo/MS_1002969 LipidMatch http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. http://purl.obolibrary.org/obo/MS_1002970 Greazy http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Open-source software for automated phospholipid tandem mass spectrometry identification. http://purl.obolibrary.org/obo/MS_1002971 LipidBlast http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library. http://purl.obolibrary.org/obo/MS_1002972 Lipid-Pro http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. http://purl.obolibrary.org/obo/MS_1002973 LipidFinder http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets. http://purl.obolibrary.org/obo/MS_1002974 LipiDex http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software An integrated software package for high-confidence lipid identification. http://purl.obolibrary.org/obo/MS_1002975 LIQUID http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software An-open source software for identifying lipids in LC-MS/MS-based lipidomics data. http://purl.obolibrary.org/obo/MS_1002976 ALEX http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1). http://purl.obolibrary.org/obo/MS_1002977 ALEX123 http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level. http://purl.obolibrary.org/obo/MS_1002979 LOBSTAHS http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers. http://purl.obolibrary.org/obo/MS_1002980 LipidQA http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species. http://purl.obolibrary.org/obo/MS_1002981 Proline http://purl.obolibrary.org/obo/MS_1001456 analysis software The Proline software suite for mass spectrometry based proteomics. http://purl.obolibrary.org/obo/MS_1002982 PepNovo http://purl.obolibrary.org/obo/MS_1001456 analysis software PepNovo tool for de novo peptide sequencing. http://purl.obolibrary.org/obo/MS_1002983 pNovo http://purl.obolibrary.org/obo/MS_1001456 analysis software pNovo tool for de novo peptide sequencing and identification using HCD spectra. http://purl.obolibrary.org/obo/MS_1002985 in-gel digestion http://purl.obolibrary.org/obo/MS_1000831 sample preparation Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes. http://purl.obolibrary.org/obo/MS_1002988 IdentiPy:RHNS http://purl.obolibrary.org/obo/MS_1001153 search engine specific score The IdentiPy result 'RHNS'. http://purl.obolibrary.org/obo/MS_1002989 IdentiPy:hyperscore http://purl.obolibrary.org/obo/MS_1001153 search engine specific score The IdentiPy result 'hyperscore'. http://purl.obolibrary.org/obo/MS_1002990 ms_deisotope http://purl.obolibrary.org/obo/MS_1001457 data processing software ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra. http://purl.obolibrary.org/obo/MS_1002991 python-psims http://purl.obolibrary.org/obo/MS_1002333 conversion software python-psims, a library for generating mzML and mzIdentML. http://purl.obolibrary.org/obo/MS_1002996 Andromeda:apl file format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Peak list file format of the Andromeda search engine. http://purl.obolibrary.org/obo/MS_1002998 LCMS-9030 http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS. http://purl.obolibrary.org/obo/MS_1002999 LCMS-8060 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu Scientific Instruments LCMS-8060 MS. http://purl.obolibrary.org/obo/MS_1003000 LCMS-8050 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu Scientific Instruments LCMS-8050 MS. http://purl.obolibrary.org/obo/MS_1003001 LCMS-8045 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu Scientific Instruments LCMS-8045 MS. http://purl.obolibrary.org/obo/MS_1003002 LCMS-8040 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu Scientific Instruments LCMS-8040 MS. http://purl.obolibrary.org/obo/MS_1003003 LCMS-2020 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu Scientific Instruments LCMS-2020. http://purl.obolibrary.org/obo/PEFF_0000024 HasAnnotationIdentifiers http://purl.obolibrary.org/obo/PEFF_0000002 PEFF file header section term PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation. http://purl.obolibrary.org/obo/PEFF_0001030 Proteoform http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers. http://purl.obolibrary.org/obo/PEFF_0001031 DisulfideBond http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications. http://purl.obolibrary.org/obo/PEFF_0001032 PEFF molecule processing keyword http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword describing the type of processing event being described. http://purl.obolibrary.org/obo/PEFF_0001033 Comment http://purl.obolibrary.org/obo/PEFF_0000003 PEFF file sequence entry term PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary. http://purl.obolibrary.org/obo/PEFF_0001034 propeptide http://purl.obolibrary.org/obo/PEFF_0001032 PEFF molecule processing keyword Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide. http://purl.obolibrary.org/obo/MS_1003591 ultra-performance liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system A system for Ultra-Performance Liquid Chromatography (UPLC), a trademark of the Waters Corporation and is largely synonymous with ultra-high performance liquid chromatography. http://purl.obolibrary.org/obo/MS_1003606 Waters liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model Waters Corporation liquid chromatography system model. http://purl.obolibrary.org/obo/MS_1003599 nano-flow liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system Nano-flow LC at a typical flow rate in the nL/min range (e.g., 50-1000 nL/min) with a typical column internal diameter of ≤ 0.1 mm, commonly used for high sensitivity, low sample volume applications. http://purl.obolibrary.org/obo/MS_1002994 Orbitrap Excedion Pro http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Orbitrap Excedion Pro. http://purl.obolibrary.org/obo/MS_1003443 ZenoTOF 8600 http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX ZenoTOF 8600 system. http://purl.obolibrary.org/obo/MS_1003444 ZenoTOF 7600+ http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX ZenoTOF 7600+ system. http://purl.obolibrary.org/obo/MS_1003445 SCIEX 7500+ http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument SCIEX 7500+ system. http://purl.obolibrary.org/obo/MS_1003447 SCIEX MS Data Converter http://purl.obolibrary.org/obo/MS_1001457 data processing software A software for converting SCIEX wiff or wiff2 format to mzML. http://purl.obolibrary.org/obo/MS_1003449 ISQ 7000 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Thermo Scientific ISQ 7000 Single Quadrupole GC-MS System. http://purl.obolibrary.org/obo/MS_1003450 FAIMS compensation voltage ramp start http://purl.obolibrary.org/obo/MS_1003254 peak attribute DC potential at the start of the FAIMS voltage ramp. http://purl.obolibrary.org/obo/MS_1003452 Ionicon Analytik instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model Ionicon Analytik instrument model. http://purl.obolibrary.org/obo/MS_1003453 JEOL instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model JEOL instrument model. http://purl.obolibrary.org/obo/MS_1003454 IONTOF instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model IONTOF instrument model. http://purl.obolibrary.org/obo/MS_1003455 PerkinElmer instrument model http://purl.obolibrary.org/obo/MS_1000031 instrument model PerkinElmer instrument model. http://purl.obolibrary.org/obo/MS_1003456 TripleTOF 6600+ http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument SCIEX TripleTOF 6600+ triple quadrupole - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003458 Triple Quad 5500+ QTRAP Ready http://purl.obolibrary.org/obo/MS_1003765 triple quadrupole linear ion trap instrument SCIEX Triple Quad 5500+ QTRAP Ready quadrupole - linear ion trap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003459 APEX-Qe http://purl.obolibrary.org/obo/MS_1003766 quadrupole fourier transform ion cyclotron resonance instrument Bruker APEX-Qe FT-ICR-MS mass spectrometer. http://purl.obolibrary.org/obo/MS_1003460 autoflex speed TOF/TOF http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker autoflex speed TOF/TOF MALDI TOF/TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003461 esquire 3000 http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker esquire 3000 ion trap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003462 maXis impact http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker maXis impact quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003463 maXis impact HD http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker maXis impact HD quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003464 maXis 3G http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker maXis 3G quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003465 solariX XR http://purl.obolibrary.org/obo/MS_1003766 quadrupole fourier transform ion cyclotron resonance instrument Bruker solariX XR FT-ICR-MS mass spectrometer. http://purl.obolibrary.org/obo/MS_1003466 amaZon SL http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker amaZon SL ion trap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003467 EVOQ DART-TQ+ http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Bruker EVOQ DART-TQ+ triple quadrupole mass spectrometer with Direct Analysis in Real Time (DART) ion source. http://purl.obolibrary.org/obo/MS_1003468 EVOQ LC-TQ http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Bruker EVOQ LC-TQ triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003469 EVOQ GC-TQ http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Bruker EVOQ GC-TQ gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003470 Toxtyper http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Bruker Toxtyper ion trap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003471 impact II VIP http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Bruker impact II VIP quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003472 ecTOF http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker ecTOF gas chromatograph - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003473 autoflex maX http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker autoflex maX MALDI TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003474 rapifleX MALDI PharmaPulse http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker rapifleX MALDI PharmaPulse MALDI TOF mass spectrometer with ultra-high-throughput screening (uHTS) capability. http://purl.obolibrary.org/obo/MS_1003475 smartfleX http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker smartfleX MALDI TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003476 neofleX http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Bruker neofleX MALDI TOF/TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003477 MALDI Biotyper http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Bruker MALDI Biotyper MALDI TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003478 scimaX http://purl.obolibrary.org/obo/MS_1003766 quadrupole fourier transform ion cyclotron resonance instrument Bruker scimaX FT-ICR-MS mass spectrometer. http://purl.obolibrary.org/obo/MS_1003479 timsMetabo http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker timsMetabo TIMS-Q-TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003480 timsUltra AIP http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker timsUltra AIP TIMS-Q-TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003481 timsOmni http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker timsOmni TIMS-Q-TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003482 timsTOF MALDI PharmaPulse http://purl.obolibrary.org/obo/MS_1003970 ion mobility quadrupole time-of-flight instrument Bruker timsTOF MALDI PharmaPulse MALDI TIMS-Q-TOF mass spectrometer with ultra-high-throughput screening (uHTS) capability. http://purl.obolibrary.org/obo/MS_1003483 4000 GC/MS http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Varian 4000 GC/MS gas chromatograph - ion trap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003484 210-MS GC/MS Ion Trap http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Varian 210-MS GC/MS Ion Trap gas chromatograph - ion trap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003485 LCMS-8030 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu LCMS-8030 triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003486 LCMS-8030 Plus http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu LCMS-8030 Plus triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003487 GCMS-QP2010 Plus http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu GCMS-QP2010 Plus gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003488 LCMS-8060NX http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu LCMS-8060NX triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003489 GCMS-TQ8050NX http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu GCMS-TQ8050NX gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003490 GCMS-TQ8040NX http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu GCMS-TQ8040NX gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003491 GCMS-TQ8040 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu GCMS-TQ8040 gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003492 GCMS-QP5000 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu GCMS-QP5000 gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003493 GCMS-QP2020 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu GCMS-QP2020 gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003494 GCMS-QP2010 Ultra http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu GCMS-QP2010 Ultra gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003495 Velos Pro http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Fisher Scientific Velos Pro ion trap - mass spectrometer. http://purl.obolibrary.org/obo/MS_1003496 MALDI LTQ Orbitrap XL http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Thermo Fisher Scientific MALDI LTQ Orbitrap XL linear ion trap - orbitrap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003497 MALDI LTQ Orbitrap Discovery http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Thermo Fisher Scientific MALDI LTQ Orbitrap Discovery linear ion trap - orbitrap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003498 TSQ Quantum Access MAX http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Fisher Scientific TSQ Quantum Access MAX triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003499 LTQ Orbitrap Velos/ETD http://purl.obolibrary.org/obo/MS_1003768 ion trap orbitrap instrument Thermo Fisher Scientific LTQ Orbitrap Velos/ETD linear ion trap - orbitrap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003500 ISQ LT http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Thermo Fisher Scientific ISQ LT gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003501 ITQ http://purl.obolibrary.org/obo/MS_1003952 ion trap instrument Thermo Fisher Scientific ITQ ion trap mass spectrometer. http://purl.obolibrary.org/obo/MS_1003502 TSQ Quantum XLS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Fisher Scientific TSQ Quantum XLS gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003503 TSQ 8000 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Thermo Fisher Scientific TSQ 8000 gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003504 DeltaPlus IRMS http://purl.obolibrary.org/obo/MS_1003949 magnetic sector instrument Thermo Fisher Scientific DeltaPlus IRMS isotope ratio mass spectrometer. http://purl.obolibrary.org/obo/MS_1003505 ACQUITY QDa http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Waters ACQUITY QDa quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003506 LCT Premier http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Waters LCT Premier time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003507 Quattro Premier XE http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters Quattro Premier XE triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003510 Synapt G1 http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters Synapt G1 quadrupole - ion mobility - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003511 Synapt G2 XS QTOF http://purl.obolibrary.org/obo/MS_1003767 quadrupole ion mobility time-of-flight instrument Waters Synapt G2 XS QTOF quadrupole - ion mobility - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003512 Xevo TQ Absolute http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters Xevo TQ Absolute triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003513 Xevo TQ Absolute XR http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Waters Xevo TQ Absolute XR triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003514 5973 MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5973 MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003516 5975 MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5975 MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003517 5975B MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5975B MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003518 5975C inert XL MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5975C inert XL MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003519 5975C MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5975C MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003520 5975T MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5975T MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003521 5977 MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5977 MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003522 5977A MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5977A MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003523 5977B MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5977B MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003524 5977C MSD http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Agilent 5977C MSD gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003525 6230 Time-of-Flight LC/MS http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Agilent 6230 Time-of-Flight LC/MS time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003527 6445 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 6445 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003528 6456 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 6456 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003529 6470 Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Agilent 6470 Triple Quadrupole LC/MS triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003530 6490A Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Agilent 6490A Triple Quadrupole LC/MS triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003531 6495 Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Agilent 6495 Triple Quadrupole LC/MS triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003532 6520 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 6520 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003533 6530 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 6530 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003534 6543 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 6543 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003535 6545XT Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 6545XT Q-TOF LC/MS quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003536 6546 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 6546 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003537 6600 Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 6600 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003538 7000C Triple Quadrupole GC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Agilent 7000C Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003539 7000D Triple Quadrupole GC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Agilent 7000D Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003540 7010 Triple Quadrupole GC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Agilent 7010 Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003541 7010B Triple Quadrupole GC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Agilent 7010B Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003542 7200 Q-TOF GC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 7200 Q-TOF GC/MS gas chromatograph - quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003543 7250 Q-TOF GC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent 7250 Q-TOF GC/MS gas chromatograph - quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003544 CE-TOFMS http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Agilent CE-TOFMS capillary electrophoresis - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003545 G3250AA Time-of-Flight LC/MS http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Agilent G3250AA Time-of-Flight LC/MS time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003546 Revident Q-TOF LC/MS http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Agilent Revident Q-TOF LC/MS quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003547 Pegasus BT 4D http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO Pegasus BT 4D GCxGC - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003548 Pegasus HT http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO Pegasus HT gas chromatograph - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003549 Pegasus IV http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument LECO Pegasus IV time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003550 PTR-TOF 8000 http://purl.obolibrary.org/obo/MS_1003452 Ionicon Analytik instrument model Ionicon Analytik PTR-TOF 8000 proton-transfer-reaction - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003551 AccuTOF GCv http://purl.obolibrary.org/obo/MS_1003453 JEOL instrument model JEOL AccuTOF GCv gas chromatograph - time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003552 TOF.SIMS 5 http://purl.obolibrary.org/obo/MS_1003454 IONTOF instrument model IONTOF TOF.SIMS 5 time-of-flight secondary ion mass spectrometer. http://purl.obolibrary.org/obo/MS_1003553 TurboMass GC/MS http://purl.obolibrary.org/obo/MS_1003455 PerkinElmer instrument model PerkinElmer TurboMass GC/MS gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003554 ThermoQuest Voyager http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Thermo Finnigan ThermoQuest Voyager gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003555 AXIMA-LNR http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Shimadzu AXIMA-LNR MALDI TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003556 AXIMA-TOF² http://purl.obolibrary.org/obo/MS_1003946 tandem time-of-flight instrument Shimadzu AXIMA-TOF² MALDI TOF/TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003557 AXIMA Resonance http://purl.obolibrary.org/obo/MS_1003764 ion trap time-of-flight instrument Shimadzu AXIMA Resonance MALDI TOF mass spectrometerwith Ion Trap for MSn. http://purl.obolibrary.org/obo/MS_1003558 MALDI-8020 http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Shimadzu MALDI-8020 benchtop MALDI TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003559 MALDI-8030 http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Shimadzu MALDI-8030 benchtop MALDI TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003560 MALDI-8020 EasyCare http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Shimadzu MALDI-8020 EasyCare benchtop MALDI TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003561 MALDI-8030 EasyCare http://purl.obolibrary.org/obo/MS_1003951 time-of-flight instrument Shimadzu MALDI-8030 EasyCare benchtop MALDI TOF mass spectrometer. http://purl.obolibrary.org/obo/MS_1003562 LCMS-2010 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu LCMS-2010 quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003563 LCMS-2050 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu LCMS-2050 quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003564 LCMS-8045RX http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu LCMS-8045RX triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003565 LCMS-8050RX http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu LCMS-8050RX triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003566 LCMS-8060RX http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu LCMS-8060RX triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003567 LCMS-8065XE http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu LCMS-8065XE triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003568 LCMS-9050 http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Shimadzu LCMS-9050 quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003569 GCMS-QP5050A http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu GCMS-QP5050A gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003570 GCMS-QP2010S http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu GCMS-QP2010S gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003571 GCMS-QP2010 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu GCMS-QP2010 gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003572 GCMS-QP2020NX http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu GCMS-QP2020NX gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003573 GCMS-QP2050 http://purl.obolibrary.org/obo/MS_1003950 quadrupole instrument Shimadzu GCMS-QP2050 gas chromatograph - quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003574 GCMS-TQ 8030 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu GCMS-TQ 8030 gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003575 GCMS-TQ 8050 http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument Shimadzu GCMS-TQ 8050 gas chromatograph - triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003576 all ions fragmentation DIA alignment http://purl.obolibrary.org/obo/MS_1000543 data processing action Associating of product ions with the precursor from which they are derived, by comparing retention time and, where appropriate, ion mobility peaks. http://purl.obolibrary.org/obo/MS_1003577 hyphenated separation http://purl.obolibrary.org/obo/MS_1000857 run attribute The methods, technology and chemistry by which a hyphenated separation system effects the separation of compounds. http://purl.obolibrary.org/obo/MS_1003579 ion-exchange chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Ion-exchange chromatography is a technique used to separate molecules based on their surface charge. The process relies on the reversible electrostatic interaction between charged molecules in a sample and an oppositely charged stationary phase, typically a resin in a column. http://purl.obolibrary.org/obo/MS_1003580 size-exclusion chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Size-exclusion chromatography (SEC), also known as gel filtration chromatography (GFC) or gel permeation chromatography (GPC), is a chromatographic technique that separates molecules based on their size or, more precisely, their hydrodynamic volume in solution. This method is primarily used for the separation of large molecules like proteins and polymers. http://purl.obolibrary.org/obo/MS_1003581 affinity chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Affinity chromatography (AC) is a highly selective separation technique used to purify specific biomolecules from complex mixtures, leveraging their unique biological or chemical interactions with an immobilized ligand. http://purl.obolibrary.org/obo/MS_1003582 reversed phase chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Reversed-phase (RP) chromatography is a technique used to separate compounds based primarily on their hydrophobicity. http://purl.obolibrary.org/obo/MS_1003583 normal phase chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Normal-phase (NP) chromatography is a technique used to separate compounds based primarily on their polarity. http://purl.obolibrary.org/obo/MS_1003584 hydrophilic interaction liquid chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Hydrophilic Interaction Liquid Chromatography (HILIC) is a chromatographic technique for the separation of polar and hydrophilic compounds. HILIC employs a polar stationary phase that absorbs water from the mobile phase to form a hydrophilic layer that retains polar analytes. http://purl.obolibrary.org/obo/MS_1003585 chiral separation liquid chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Chiral separation in liquid chromatography is the process of resolving enantiomers. http://purl.obolibrary.org/obo/MS_1003586 mixed mode chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Mixed-mode separation in liquid chromatography uses stationary phases that combine multiple types of interactions to retain and separate compounds. http://purl.obolibrary.org/obo/MS_1003587 hydrophobic interaction chromatography http://purl.obolibrary.org/obo/MS_1002271 liquid chromatography separation Hydrophobic Interaction Chromatography (HIC) is a type of chromatography used to separate biomolecules, typically proteins, based on their differences in surface hydrophobicity. http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system http://purl.obolibrary.org/obo/MS_1003737 separation system Liquid chromatography (LC) is an analytical technique used to separate a mixture into its individual components for identification, quantification, and purification. The separation is based on the differential interactions of the sample compounds with a liquid mobile phase and a solid stationary phase. http://purl.obolibrary.org/obo/MS_1003590 high-performance liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system A system for High-Performance Liquid Chromatography (HPLC), a widely used analytical chemistry technique for separating, identifying, and quantifying individual components in a liquid mixture. http://purl.obolibrary.org/obo/MS_1003592 ultra-high performance liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system A system for Ultra-High Performance Liquid Chromatography (UHPLC), an advanced form of high-performance liquid chromatography designed to achieve significantly faster, higher-resolution, and more sensitive separations. It is primarily achieved by innovations in particle chemistry and systemation capable of handling ultra-high pressures. http://purl.obolibrary.org/obo/MS_1003593 fast protein liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system A system for Fast Protein Liquid Chromatography (FPLC), a versatile and widely used medium-pressure chromatography technique primarily employed for the separation and purification of biomolecules, especially proteins. It operates under low to moderate pressures, making it suitable for labile proteins and other large biomolecules that might be denatured by the high pressures and organic solvents often used in high-performance liquid chromatography. http://purl.obolibrary.org/obo/MS_1003594 three-dimensional liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system A system for Three-dimensional liquid chromatography (3D-LC), an advanced separation technique that combines three distinct liquid chromatography (LC) methods to achieve significantly enhanced separation power for complex mixtures, particularly in fields like proteomics. http://purl.obolibrary.org/obo/MS_1003595 planar chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system A system for on-line planar chromatography. http://purl.obolibrary.org/obo/MS_1003596 thin layer chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system A system for on-line Thin Layer Chromatography (TLC), based upon a widely used, simple, and cost-effective analytical technique for separating and identifying components in a mixture. http://purl.obolibrary.org/obo/MS_1003597 high-performance thin layer chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system A system for on-line High-Performance Thin Layer Chromatography (HPTLC), an advanced and refined version of traditional Thin Layer Chromatography (TLC), designed to offer significantly improved performance in terms of resolution, sensitivity, and reproducibility. It utilizes finer and more uniformly sized stationary phase particles, leading to more efficient separations and more accurate quantitative analysis. http://purl.obolibrary.org/obo/MS_1003598 two-dimensional liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system A system for two-dimensional liquid chromatography (2D-LC), also often referred to as LC-LC or LC×LC, an advanced analytical technique that combines two different liquid chromatography methods in series to achieve enhanced separation of complex mixtures. It offers significantly higher resolving power and peak capacity compared to conventional one-dimensional liquid chromatography (1D-LC). http://purl.obolibrary.org/obo/MS_1003600 capillary-flow liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system Capillary-flow LC at a typical flow rate of 2-10 µL/min with a typical column internal diameter of 0.3-0.5 mm, commonly used for high sensitivity applications. http://purl.obolibrary.org/obo/MS_1003601 micro-flow liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system Micro-flow, or microbore, LC at a typical flow rate of 10-50 µL/min with a typical column internal diameter of 1.0 mm, commonly used for increased sensitivity application and lower solvent consumption. http://purl.obolibrary.org/obo/MS_1003602 analytical liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system Analytical scale LC at a typical flow rate between 0.2- 3 mL/min with a typical column internal diameter of 2.1-4.6 mm, commonly used in typical LC methodology. http://purl.obolibrary.org/obo/MS_1003603 semi-preparative liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system Semi-preparative LC at a typical flow rate between 5-50 mL/min with a typical column internal diameter of 10 mm, commonly used for the small scale purification and isolation of compounds. http://purl.obolibrary.org/obo/MS_1003604 preparative liquid chromatography system http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system Preparative LC at a typical flow rate of > 50 mL/min with a typical column internal diameter of > 20 mm, commonly used for the large scale purification and isolation of bulk quantities of target compounds. http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003589 liquid chromatography system Liquid chromatography system model name not including the vendor's name. http://purl.obolibrary.org/obo/MS_1003607 timsControl http://purl.obolibrary.org/obo/MS_1001455 acquisition software Bruker software for data acquisition. http://purl.obolibrary.org/obo/MS_1003608 MetaboScape http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker software for untargeted metabolomics and lipidomics data analysis. http://purl.obolibrary.org/obo/MS_1003609 TASQ http://purl.obolibrary.org/obo/MS_1001457 data processing software Bruker software for target screening and quantitation. http://purl.obolibrary.org/obo/MS_1003610 mzPeak format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format Proteomics Standards Initiatve mzPeak file format. http://purl.obolibrary.org/obo/MS_1003611 imzML format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format IMSIS imzML imaging file format. http://purl.obolibrary.org/obo/MS_1003612 InstaNovo http://purl.obolibrary.org/obo/MS_1001456 analysis software InstaNovo is a deep learning based tool using a Transformer architecture for de novo peptide sequencing. http://purl.obolibrary.org/obo/MS_1003613 InstaNovo+ http://purl.obolibrary.org/obo/MS_1001456 analysis software InstaNovo+ is a deep learning based tool using a Diffusion architecture for de novo peptide sequencing. http://purl.obolibrary.org/obo/MS_1003615 Advion liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model Advion Interchim Scientific liquid chromatography system model. http://purl.obolibrary.org/obo/MS_1003616 AVANT http://purl.obolibrary.org/obo/MS_1003615 Advion liquid chromatography system model Advion AVANT UHPLC system. http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model Agilent Technologies liquid chromatography system model. http://purl.obolibrary.org/obo/MS_1003618 1100 Series http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1100 Series HPLC system. http://purl.obolibrary.org/obo/MS_1003619 1200 Series http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1200 Series HPLC system. http://purl.obolibrary.org/obo/MS_1003620 1200 Series HPLC-Chip http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1200 Series HPLC-Chip system. http://purl.obolibrary.org/obo/MS_1003621 1200 Series Rapid Resolution http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1200 Series Rapid Resolution RRLC system. http://purl.obolibrary.org/obo/MS_1003622 1200 RR Series II http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1200 RR Series II RRLC system. http://purl.obolibrary.org/obo/MS_1003623 1200 SL http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1200 SL RRLC system. http://purl.obolibrary.org/obo/MS_1003624 1220 Infinity http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1220 Infinity UHPLC system. http://purl.obolibrary.org/obo/MS_1003625 1260 Infinity II http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1260 Infinity II UHPLC system. http://purl.obolibrary.org/obo/MS_1003626 1260 Infinity http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1260 Infinity UHPLC system. http://purl.obolibrary.org/obo/MS_1003627 1290 Infinity 2D-LC http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1290 Infinity 2D-LC 2D-LC UHPLC system. http://purl.obolibrary.org/obo/MS_1003628 1290 Infinity http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1290 Infinity UHPLC system. http://purl.obolibrary.org/obo/MS_1003629 1290 Infinity II 2D-LC http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1290 Infinity II 2D-LC 2D-LC UHPLC system. http://purl.obolibrary.org/obo/MS_1003630 1290 Infinity II http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1290 Infinity II UHPLC system. http://purl.obolibrary.org/obo/MS_1003631 1200 Infinity http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1200 Infinity UHPLC system. http://purl.obolibrary.org/obo/MS_1003632 1220 Infinity II http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1220 Infinity II UHPLC system. http://purl.obolibrary.org/obo/MS_1003633 1260 Infinity III http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1260 Infinity III UHPLC system. http://purl.obolibrary.org/obo/MS_1003634 1260 Infinity III Prime http://purl.obolibrary.org/obo/MS_1003617 Agilent liquid chromatography system model Agilent 1260 Infinity III Prime UHPLC system. http://purl.obolibrary.org/obo/MS_1003635 adduct ion monoisotopic mass http://purl.obolibrary.org/obo/MS_1003243 adduct ion mass The theoretical monoisotopic mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's monoisotopic mass plus the mass of a proton). http://purl.obolibrary.org/obo/MS_1003636 adduct ion average mass http://purl.obolibrary.org/obo/MS_1003243 adduct ion mass The theoretical average mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's average mass plus the average mass of a hydrogen ion). http://purl.obolibrary.org/obo/MS_1003637 theoretical neutral monoisotopic mass http://purl.obolibrary.org/obo/MS_1001117 theoretical neutral mass The theoretical neutral monoisotopic mass of the molecule (e.g. the peptide sequence and its modifications), not including its charge carrier. http://purl.obolibrary.org/obo/MS_1003638 theoretical neutral average mass http://purl.obolibrary.org/obo/MS_1001117 theoretical neutral mass The theoretical neutral average mass of the molecule (e.g. the peptide sequence and its modifications), not including its charge carrier. http://purl.obolibrary.org/obo/MS_1003639 Beckman Coulter liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model Beckman Coulter, Inc. liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003640 System Gold http://purl.obolibrary.org/obo/MS_1003639 Beckman Coulter liquid chromatography system model Beckman Coulter System Gold HPLC system. http://purl.obolibrary.org/obo/MS_1003641 Bruker liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model Bruker Corporation liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003642 Elute http://purl.obolibrary.org/obo/MS_1003641 Bruker liquid chromatography system model Bruker Elute UHPLC system. http://purl.obolibrary.org/obo/MS_1003643 Elute HT http://purl.obolibrary.org/obo/MS_1003641 Bruker liquid chromatography system model Bruker Elute HT UHPLC system. http://purl.obolibrary.org/obo/MS_1003644 Elute OLE http://purl.obolibrary.org/obo/MS_1003641 Bruker liquid chromatography system model Bruker Elute OLE UHPLC system. http://purl.obolibrary.org/obo/MS_1003645 Elute SP http://purl.obolibrary.org/obo/MS_1003641 Bruker liquid chromatography system model Bruker Elute SP HPLC system. http://purl.obolibrary.org/obo/MS_1003646 nanoElute 2 http://purl.obolibrary.org/obo/MS_1003641 Bruker liquid chromatography system model Bruker nanoElute 2 HPLC system. http://purl.obolibrary.org/obo/MS_1003647 proteoElute http://purl.obolibrary.org/obo/MS_1003641 Bruker liquid chromatography system model Bruker proteoElute UHPLC system. http://purl.obolibrary.org/obo/MS_1003648 Michrom BioResources Paradigm MS4 http://purl.obolibrary.org/obo/MS_1003641 Bruker liquid chromatography system model Bruker Michrom BioResources Paradigm MS4 2D-LC HPLC system. http://purl.obolibrary.org/obo/MS_1003649 Michrom Advance nanoflow http://purl.obolibrary.org/obo/MS_1003641 Bruker liquid chromatography system model Bruker Michrom Advance nanoflow UHPLC system. http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model SCIEX liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003651 ExionLC http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX ExionLC HPLC system. http://purl.obolibrary.org/obo/MS_1003652 ExionLC AC http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX ExionLC AC UHPLC system. http://purl.obolibrary.org/obo/MS_1003653 ExionLC AD http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX ExionLC AD UHPLC system. http://purl.obolibrary.org/obo/MS_1003654 ExionLC AE http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX ExionLC AE UHPLC system. http://purl.obolibrary.org/obo/MS_1003655 ExionLC 2.0 http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX ExionLC 2.0 UHPLC system. http://purl.obolibrary.org/obo/MS_1003656 ExionLC 2.0+ http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX ExionLC 2.0+ UHPLC system. http://purl.obolibrary.org/obo/MS_1003657 Eksigent ekspert nanoLC 400 http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX Eksigent ekspert nanoLC 400 HPLC system. http://purl.obolibrary.org/obo/MS_1003658 Eksigent ekspert nanoLC 425 http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX Eksigent ekspert nanoLC 425 HPLC system. http://purl.obolibrary.org/obo/MS_1003659 Eksigent ekspret ultraLC 100 http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX Eksigent ekspret ultraLC 100 UHPLC system. http://purl.obolibrary.org/obo/MS_1003660 Eksigent ekspert ultraLC 100-XL http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX Eksigent ekspert ultraLC 100-XL UHPLC system. http://purl.obolibrary.org/obo/MS_1003661 Eksigent ekspert ultraLC 110 http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX Eksigent ekspert ultraLC 110 UHPLC system. http://purl.obolibrary.org/obo/MS_1003662 Eksigent NanoLC-Ultra 2D http://purl.obolibrary.org/obo/MS_1003650 SCIEX liquid chromatography system model SCIEX Eksigent NanoLC-Ultra 2D 2D-LC UHPLC system. http://purl.obolibrary.org/obo/MS_1003663 Hitachi liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model Hitachi, Ltd. liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003664 L-7100 http://purl.obolibrary.org/obo/MS_1003663 Hitachi liquid chromatography system model Hitachi L-7100 HPLC pump. http://purl.obolibrary.org/obo/MS_1003665 LaChrom Ultra http://purl.obolibrary.org/obo/MS_1003663 Hitachi liquid chromatography system model Hitachi LaChrom Ultra UHPLC system. http://purl.obolibrary.org/obo/MS_1003666 Chromaster http://purl.obolibrary.org/obo/MS_1003663 Hitachi liquid chromatography system model Hitachi Chromaster HPLC system. http://purl.obolibrary.org/obo/MS_1003667 Chromaster RS http://purl.obolibrary.org/obo/MS_1003663 Hitachi liquid chromatography system model Hitachi Chromaster RS UHPLC system. http://purl.obolibrary.org/obo/MS_1003668 JASCO liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model JASCO, Inc. liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003669 X-LC Series http://purl.obolibrary.org/obo/MS_1003668 JASCO liquid chromatography system model JASCO X-LC Series UHPLC system. http://purl.obolibrary.org/obo/MS_1003670 LC-4000 Series http://purl.obolibrary.org/obo/MS_1003668 JASCO liquid chromatography system model JASCO LC-4000 Series UHPLC system. http://purl.obolibrary.org/obo/MS_1003671 LC-2000 Series http://purl.obolibrary.org/obo/MS_1003668 JASCO liquid chromatography system model JASCO LC-2000 Series HPLC system. http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003605 liquid chromatography system model Shimadzu Corporation liquid chromatography system model http://purl.obolibrary.org/obo/MS_1003673 LC-10 http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu LC-10 HPLC system. http://purl.obolibrary.org/obo/MS_1003674 Nexera LC-20 http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu Nexera LC-20 HPLC system. http://purl.obolibrary.org/obo/MS_1003675 Nexera LC-30 http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu Nexera LC-30 UHPLC system. http://purl.obolibrary.org/obo/MS_1003676 Nexera X2 LC-30 http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu Nexera X2 LC-30 UHPLC system. http://purl.obolibrary.org/obo/MS_1003677 Nexera LC-40 http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu Nexera LC-40 UHPLC system. http://purl.obolibrary.org/obo/MS_1003678 Prominence LC-20 http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu Prominence LC-20 HPLC system. http://purl.obolibrary.org/obo/MS_1003679 Prominence UFLC http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu Prominence UFLC HPLC system. http://purl.obolibrary.org/obo/MS_1003680 Prominence UFLC XR http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu Prominence UFLC XR UHPLC system. http://purl.obolibrary.org/obo/MS_1003681 LC-2040C 3D Nexera-i http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu LC-2040C 3D Nexera-i HPLC system. http://purl.obolibrary.org/obo/MS_1003682 Prominence Plus LC-30 http://purl.obolibrary.org/obo/MS_1003672 Shimadzu liquid chromatography system model Shimadzu Prominence Plus LC-30 HPLC system. http://purl.obolibrary.org/obo/MS_4000190 MS1 TIC quantile RT http://purl.obolibrary.org/obo/MS_4000004 n-tuple The amount of time elapsed since the start of the data acquisition until the implied quantile of all MS1 TIC has been accumulated. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000191 MS2 TIC quantile RT http://purl.obolibrary.org/obo/MS_4000004 n-tuple The amount of time elapsed since the start of the data acquisition until the implied quantile of all MS2 TIC has been accumulated. The number of values in the tuple implies the quantile mode. http://purl.obolibrary.org/obo/MS_4000192 MS1 median cycle time http://purl.obolibrary.org/obo/MS_4000003 single value The median time between consecutive MS1 scans across the full run. http://purl.obolibrary.org/obo/MS_4000193 DIA isolation window median cycle time http://purl.obolibrary.org/obo/MS_4000003 single value The median time between consecutive measurements of the same DIA isolation window across the full run. http://purl.obolibrary.org/obo/MS_4000194 DIA isolation window count http://purl.obolibrary.org/obo/MS_4000003 single value The number of distinct DIA isolation windows (i.e. sharing the same low m/z boundary, high m/z boundary, and ion mobility parameters). http://purl.obolibrary.org/obo/MS_4000197 DIA isolation window half TIC RT http://purl.obolibrary.org/obo/MS_4000004 n-tuple The minimum and maximum retention time in which at least half of the TIC for any given DIA isolation window compared to the full TIC in this isolation window has been collected. http://purl.obolibrary.org/obo/MS_4000198 DIA isolation window TIC http://purl.obolibrary.org/obo/MS_4000004 n-tuple The minimum and maximum TIC collected in any given DIA isolation window. http://purl.obolibrary.org/obo/MS_4000199 DIA isolation window peak count http://purl.obolibrary.org/obo/MS_4000004 n-tuple For each DIA isolation window, we compute the median number of peaks per MS/MS measurement. This metric reports the lowest and highest peak count medians among the isolation windows. http://purl.obolibrary.org/obo/MS_4000201 run outlier score LoOP http://purl.obolibrary.org/obo/MS_4000005 table Outlier score for MS runs based on the local outlier probabilities (LoOP) algorithm applied to QC metrics from all runs. http://purl.obolibrary.org/obo/MS_4000202 base peak intensity maximum http://purl.obolibrary.org/obo/MS_4000003 single value The maximum base peak intensity (MS:1000505) of all spectra in a single run. http://purl.obolibrary.org/obo/MS_4000203 base peak intensity maxima per time ranges http://purl.obolibrary.org/obo/MS_4000005 table The maximum base peak intensity (MS:1000505) of all spectra in a single run in the given retention time ranges. The time windows are specified by the 2nd column defining the start time in seconds and the 3rd column defining the duration in seconds. To define a range from a starting time until the run's end, -1 may be used for the duration with 0 for the start. http://purl.obolibrary.org/obo/MS_4000204 total ion current maximum http://purl.obolibrary.org/obo/MS_4000003 single value The maximum total ion current (MS:1000285) of all spectra in a single run. http://purl.obolibrary.org/obo/MS_4000205 total ion current maxima per time ranges http://purl.obolibrary.org/obo/MS_4000005 table The maximum total ion current (MS:1000285) of all spectra in a single run in the given retention time ranges. The time windows are specified by the 2nd column defining the start time in seconds and the 3rd column defining the duration in seconds. To define a range from a starting time until the run's end, -1 may be used for the duration with 0 for the start. http://purl.obolibrary.org/obo/MS_4000206 precursor ppm deviation distribution http://purl.obolibrary.org/obo/MS_4000004 n-tuple The quantiles of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied. E.g. one value triplet represents the quartiles Q1, Q2, Q3. http://purl.obolibrary.org/obo/MS_4000207 detected quantification data points charges fractions http://purl.obolibrary.org/obo/MS_4000005 table The fraction of all data points detected for quantification purposes within the run for each specified charge state. The fractions [0,1] are given in the 'fraction' column, corresponding charges in the 'charge state' column. The highest charge state is to be interpreted as that charge state or higher. http://purl.obolibrary.org/obo/MS_4000208 identified quantification data points charges fractions http://purl.obolibrary.org/obo/MS_4000005 table The fraction of all data points detected and identified for quantification purposes within the run for each specified charge state. The fractions [0,1] are given in the 'fraction' column, corresponding charges in the 'charge state' column. The highest charge state is to be interpreted as that charge state or higher. http://purl.obolibrary.org/obo/MS_4000209 peptide spectrum matches charges fractions http://purl.obolibrary.org/obo/MS_4000005 table The fraction of filtered peptide spectrum matches (PSMs) within the run for each specified charge state. The fractions [0,1] are given in the 'fraction' column, corresponding charges in the 'charge state' column. The highest charge state is to be interpreted as that charge state or higher. The numbers here are recorded after any filtering for PSM level quality (e.g. FDR filtering). http://purl.obolibrary.org/obo/MS_4000210 vacuum pump pressure http://purl.obolibrary.org/obo/MS_4000005 table The vacuum pump pressure of a run, defined by the retention times and respectively applied pressures. The values are similar to the ones saved in MS:1000821, but using a tabular representation. http://purl.obolibrary.org/obo/MS_4000211 MS1 total ion current http://purl.obolibrary.org/obo/MS_4000005 table Tabular representation of the total ion current (TIC) of the MS1 spectra. It is a tabular representation of the total ion current detected in each of a series of mass spectra versus time (similar to the MS:1000235, but a mzQC valid table), using only the MS1 spectra. http://purl.obolibrary.org/obo/MS_4000212 MS2 total ion current http://purl.obolibrary.org/obo/MS_4000005 table Tabular representation of the total ion current (TIC) of the MS2 spectra. It is a tabular representation of the total ion current detected in each of a series of mass spectra versus time (similar to the MS:1000235, but a mzQC valid table), using only the MS2 spectra. http://purl.obolibrary.org/obo/MS_4000213 characteristics of spike in and reference peptide http://purl.obolibrary.org/obo/MS_4000005 table Observed and expected characteristics for spiked in or reference peptides. The expected peptides are encoded by proforma peptidoform sequence (MS:1003169). The 'predicted retention time' should be interpreted as the expected retention time of a reference measurement. http://purl.obolibrary.org/obo/MS_4000214 number of all identified accessions in all ambiguity groups http://purl.obolibrary.org/obo/MS_4000003 single value The number of accessions in identified protein ambiguity groups that have been identified. This is the number of accessions in the groups, which were counted in 'MS:1002404 ! count of identified proteins', which hence must be greater or equal to this number. http://purl.obolibrary.org/obo/MS_4000215 missed cleavages fractions http://purl.obolibrary.org/obo/MS_4000005 table The fraction of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective fraction of such peptides identified in the 'fraction' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher. http://purl.obolibrary.org/obo/MS_1002851 Other type file URI http://purl.obolibrary.org/obo/MS_1002845 Associated file URI URI of one file labeled as 'Other', associated to one PX submission. http://purl.obolibrary.org/obo/MS_1002856 Supported dataset by repository http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission. http://purl.obolibrary.org/obo/MS_1002926 TopPIC:thread number http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Number of threads used in TopPIC. http://purl.obolibrary.org/obo/MS_1003117 OpenMS:Target-decoy protein q-value http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins The OpenMS Target-decoy q-values at protein level http://purl.obolibrary.org/obo/MS_1003232 PeakForest http://purl.obolibrary.org/obo/MS_1002878 small molecule analysis software comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB). http://purl.obolibrary.org/obo/MS_1002957 isotopomer MS peak http://purl.obolibrary.org/obo/MS_1002956 isotopic ion MS peak The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'. http://purl.obolibrary.org/obo/MS_1002959 isomer http://purl.obolibrary.org/obo/MS_1000859 molecule One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae. http://purl.obolibrary.org/obo/MS_1002900 feature format http://purl.obolibrary.org/obo/MS_1000560 mass spectrometer file format TopFD feature file format. http://purl.obolibrary.org/obo/MS_1002913 TopPIC:fixed modification http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter Fixed modifications for TopPIC searching. http://purl.obolibrary.org/obo/MS_1003023 OpenPepXL http://purl.obolibrary.org/obo/MS_1000752 TOPP software Cross-Linking MS search engine. http://purl.obolibrary.org/obo/MS_1003024 OpenPepXL:score http://purl.obolibrary.org/obo/MS_1001153 search engine specific score The OpenPepXL score for a crosslink spectrum match. http://purl.obolibrary.org/obo/MS_1003026 named element in mzIdentML http://purl.obolibrary.org/obo/MS_1003025 named element A named element that is an attribute in a mzIdentML file. http://purl.obolibrary.org/obo/MS_1003027 named element in mzML http://purl.obolibrary.org/obo/MS_1003025 named element A named element that is an attribute in a mzML file. http://purl.obolibrary.org/obo/MS_1003189 library description http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute Extended free-text description of the library http://purl.obolibrary.org/obo/MS_1003738 5975C http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model Agilent 5975C gas chromatograph. http://purl.obolibrary.org/obo/MS_1003739 5975T http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model Agilent 5975T gas chromatograph. http://purl.obolibrary.org/obo/MS_1003740 6890 http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model Agilent 6890 gas chromatograph. http://purl.obolibrary.org/obo/MS_1003741 7890A http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model Agilent 7890A gas chromatograph. http://purl.obolibrary.org/obo/MS_1003742 7890B http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model Agilent 7890B gas chromatograph. http://purl.obolibrary.org/obo/MS_1003743 8860 http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model Agilent 8860 gas chromatograph. http://purl.obolibrary.org/obo/MS_1003744 8890B http://purl.obolibrary.org/obo/MS_1003731 Agilent gas chromatography system model Agilent 8890B gas chromatograph. http://purl.obolibrary.org/obo/MS_1003745 Hewlett Packard gas chromatography system model http://purl.obolibrary.org/obo/MS_1003730 gas chromatography system model Hewlett Packard gas chromatography system model. http://purl.obolibrary.org/obo/MS_1003746 5890 Series http://purl.obolibrary.org/obo/MS_1003745 Hewlett Packard gas chromatography system model Hewlett Packard 5890 Series gas chromatograph. http://purl.obolibrary.org/obo/MS_1003747 5890 Series II http://purl.obolibrary.org/obo/MS_1003745 Hewlett Packard gas chromatography system model Hewlett Packard 5890 Series II gas chromatograph. http://purl.obolibrary.org/obo/MS_1003748 PerkinElmer gas chromatography system model http://purl.obolibrary.org/obo/MS_1003730 gas chromatography system model PerkinElmer gas chromatography system model. http://purl.obolibrary.org/obo/MS_1003749 AutoSystem XL GC http://purl.obolibrary.org/obo/MS_1003748 PerkinElmer gas chromatography system model PerkinElmer AutoSystem XL GC gas chromatograph. http://purl.obolibrary.org/obo/MS_1003750 Shimadzu gas chromatography system model http://purl.obolibrary.org/obo/MS_1003730 gas chromatography system model Shimadzu Corporation gas chromatography system model. http://purl.obolibrary.org/obo/MS_1003751 GC-2010 Plus http://purl.obolibrary.org/obo/MS_1003750 Shimadzu gas chromatography system model Shimadzu GC-2010 Plus gas chromatograph. http://purl.obolibrary.org/obo/MS_1003752 GC-2010 Pro http://purl.obolibrary.org/obo/MS_1003750 Shimadzu gas chromatography system model Shimadzu GC-2010 Pro gas chromatograph. http://purl.obolibrary.org/obo/MS_1003753 GC-17A http://purl.obolibrary.org/obo/MS_1003750 Shimadzu gas chromatography system model Shimadzu GC-17A gas chromatograph. http://purl.obolibrary.org/obo/MS_1003754 GC-2010 http://purl.obolibrary.org/obo/MS_1003750 Shimadzu gas chromatography system model Shimadzu GC-2010 gas chromatograph. http://purl.obolibrary.org/obo/MS_1003755 Thermo Scientific gas chromatography system model http://purl.obolibrary.org/obo/MS_1003730 gas chromatography system model Thermo Scientific gas chromatography system model. http://purl.obolibrary.org/obo/MS_1003756 TRACE 1300 http://purl.obolibrary.org/obo/MS_1003755 Thermo Scientific gas chromatography system model Thermo TRACE 1300 gas chromatograph. http://purl.obolibrary.org/obo/MS_1003757 TRACE 1310 http://purl.obolibrary.org/obo/MS_1003755 Thermo Scientific gas chromatography system model Thermo TRACE 1310 gas chromatograph. http://purl.obolibrary.org/obo/MS_1003758 TRACE GC http://purl.obolibrary.org/obo/MS_1003755 Thermo Scientific gas chromatography system model Thermo TRACE GC gas chromatograph. http://purl.obolibrary.org/obo/MS_1003759 TRACE GC Ultra http://purl.obolibrary.org/obo/MS_1003755 Thermo Scientific gas chromatography system model Thermo TRACE GC Ultra gas chromatograph. http://purl.obolibrary.org/obo/MS_1003760 FOCUS GC http://purl.obolibrary.org/obo/MS_1003755 Thermo Scientific gas chromatography system model Thermo FOCUS GC gas chromatograph. http://purl.obolibrary.org/obo/MS_1003774 mixed polarity acquisition http://purl.obolibrary.org/obo/MS_1003776 acquisition polarity The scans of a run include both positive and negative polarity acquisitions in a pattern that is not strictly alternating, such as discrete blocks of each polarity, irregular switching sequences, or other non-alternating arrangements. http://purl.obolibrary.org/obo/MS_1003775 secondary electrospray ionization http://purl.obolibrary.org/obo/MS_1000240 atmospheric pressure ionization Secondary electrospray ionization (SESI) is an atmospheric pressure ionization (API) technique that uses a primary nano-electrospray plume of solvent ions to ionize neutral gaseous molecules in the gas phase via efficient proton transfer reactions. Operating at atmospheric pressure, SESI allows for the sensitive and real-time detection of volatile organic compounds (VOCs) and vapors with minimal sample preparation, making it ideal for applications like breath analysis and environmental monitoring. http://purl.obolibrary.org/obo/MS_1002862 Reprocessed subset dataset http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed. http://purl.obolibrary.org/obo/MS_1002845 Associated file URI http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter URI of one external file associated to the PRIDE experiment (maybe through a PX submission). http://purl.obolibrary.org/obo/MS_1002858 Dataset with its publication pending http://purl.obolibrary.org/obo/MS_1002844 Experiment additional parameter A dataset which has an associated manuscript pending for publication. http://purl.obolibrary.org/obo/MS_1002848 Result file URI http://purl.obolibrary.org/obo/MS_1002845 Associated file URI URI of one file labeled as 'Result', associated to one PX submission. http://purl.obolibrary.org/obo/MS_1002895 small molecule identification attribute http://purl.obolibrary.org/obo/MS_1002694 single identification result attribute Compound identification information. http://purl.obolibrary.org/obo/MS_1002898 Shimadzu Biotech QTOF nativeID format http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Native format defined by scan=xsd:nonNegativeInteger. http://purl.obolibrary.org/obo/MS_1002897 isotopomer peak http://purl.obolibrary.org/obo/MS_1000231 peak OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'. http://purl.obolibrary.org/obo/MS_1002978 LIMSA http://purl.obolibrary.org/obo/MS_1002964 lipidomics analysis software Software tool for the quantitative analysis of mass spectrometric lipidome data. http://purl.obolibrary.org/obo/MS_1002914 TopPIC:N-term form http://purl.obolibrary.org/obo/MS_1002912 TopPIC input parameter N-terminal forms of proteins allowed in TopPIC searching. http://purl.obolibrary.org/obo/MS_1003030 Mascot:MinNumSigUniqueSeqs http://purl.obolibrary.org/obo/MS_1002095 Mascot input parameter Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'. http://purl.obolibrary.org/obo/MS_1000935 6470A Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1000936 6470B Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1000937 6495C Triple Quadrupole LC/MS http://purl.obolibrary.org/obo/MS_1003762 triple quadrupole instrument The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. http://purl.obolibrary.org/obo/MS_1003202 BiblioSpec http://purl.obolibrary.org/obo/MS_1003207 library creation software A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington http://purl.obolibrary.org/obo/MS_1003237 library spectrum key http://purl.obolibrary.org/obo/MS_1003234 library spectrum attribute An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library. http://purl.obolibrary.org/obo/MS_1003238 library analyte attribute set http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library http://purl.obolibrary.org/obo/MS_1003239 library interpretation attribute set http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library http://purl.obolibrary.org/obo/MS_1003240 peak intensity transform http://purl.obolibrary.org/obo/MS_1000543 data processing action A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores http://purl.obolibrary.org/obo/MS_1003241 square root transform http://purl.obolibrary.org/obo/MS_1003240 peak intensity transform A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots http://purl.obolibrary.org/obo/MS_1003242 rank transform http://purl.obolibrary.org/obo/MS_1003240 peak intensity transform A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks http://purl.obolibrary.org/obo/MS_1003243 adduct ion mass http://purl.obolibrary.org/obo/MS_1003056 adduct ion property The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's mass plus the mass of a proton) http://purl.obolibrary.org/obo/MS_1003244 peptide accession number http://purl.obolibrary.org/obo/MS_1003050 peptidoform attribute Accession number (e.g. in PeptideAtlas) of the peptide sequence http://purl.obolibrary.org/obo/MS_1003245 Q Exactive UHMR http://purl.obolibrary.org/obo/MS_1003769 quadrupole orbitrap instrument Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS. http://purl.obolibrary.org/obo/MS_1003246 ultraviolet photodissociation http://purl.obolibrary.org/obo/MS_1000435 photodissociation Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons. http://purl.obolibrary.org/obo/MS_1003247 negative electron transfer dissociation http://purl.obolibrary.org/obo/MS_1000044 dissociation method A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation. http://purl.obolibrary.org/obo/MS_1003248 proton transfer reaction http://purl.obolibrary.org/obo/MS_1000008 ionization type Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation. http://purl.obolibrary.org/obo/MS_1003249 proton transfer charge reduction http://purl.obolibrary.org/obo/MS_1000008 ionization type Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte. http://purl.obolibrary.org/obo/MS_1003250 count of identified peptidoforms http://purl.obolibrary.org/obo/MS_4000003 single value The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence. http://purl.obolibrary.org/obo/MS_1003251 count of identified spectra http://purl.obolibrary.org/obo/MS_4000003 single value The number of spectra that pass the threshold to be considered identified with sufficient confidence. http://purl.obolibrary.org/obo/MS_1003252 Xevo G2-XS QTof http://purl.obolibrary.org/obo/MS_1003763 quadrupole time-of-flight instrument Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer. http://purl.obolibrary.org/obo/MS_1003253 DIA-NN http://purl.obolibrary.org/obo/MS_1003207 library creation software A universal software for data-independent acquisition (DIA) proteomics data processing http://purl.obolibrary.org/obo/MS_1003255 pre-decharged charge state http://purl.obolibrary.org/obo/MS_1003254 peak attribute For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution. http://purl.obolibrary.org/obo/MS_1003257 library spectrum cross reference http://purl.obolibrary.org/obo/MS_1003234 library spectrum attribute A link from one spectrum to another spectrum of interest http://purl.obolibrary.org/obo/MS_1003258 related spectrum http://purl.obolibrary.org/obo/MS_1003257 library spectrum cross reference A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar. http://purl.obolibrary.org/obo/MS_1003259 related spectrum keys http://purl.obolibrary.org/obo/MS_1003258 related spectrum A list of cross references to a related spectrum in the same library, in the form of the library spectrum key. http://purl.obolibrary.org/obo/MS_1003260 related spectrum USI http://purl.obolibrary.org/obo/MS_1003258 related spectrum A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier http://purl.obolibrary.org/obo/MS_1003262 similar spectrum http://purl.obolibrary.org/obo/MS_1003257 library spectrum cross reference A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion. http://purl.obolibrary.org/obo/MS_1003263 similar spectrum keys http://purl.obolibrary.org/obo/MS_1003262 similar spectrum A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key. http://purl.obolibrary.org/obo/MS_1003264 similar spectrum USI http://purl.obolibrary.org/obo/MS_1003262 similar spectrum A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier http://purl.obolibrary.org/obo/MS_1003267 spectrum cluster key http://purl.obolibrary.org/obo/MS_1003266 spectrum cluster attribute An ordinal number uniquely identifying a spectrum cluster. It should start with 1. http://purl.obolibrary.org/obo/MS_1003268 spectrum cluster member spectrum keys http://purl.obolibrary.org/obo/MS_1003266 spectrum cluster attribute A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library. http://purl.obolibrary.org/obo/MS_1003269 spectrum cluster member USI http://purl.obolibrary.org/obo/MS_1003266 spectrum cluster attribute A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier. http://purl.obolibrary.org/obo/MS_1003270 proforma peptidoform ion notation http://purl.obolibrary.org/obo/MS_1003256 peptidoform ion attribute A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type. http://purl.obolibrary.org/obo/MS_4000068 spectra half-TIC http://purl.obolibrary.org/obo/MS_4000005 table The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well. http://purl.obolibrary.org/obo/MS_4000069 m/z acquisition range http://purl.obolibrary.org/obo/MS_4000004 n-tuple Upper and lower limit of m/z precursor values at which MSn spectra are recorded. http://purl.obolibrary.org/obo/MS_4000070 retention time acquisition range http://purl.obolibrary.org/obo/MS_4000004 n-tuple Upper and lower limit of retention time at which spectra are recorded. http://purl.obolibrary.org/obo/MS_4000071 number of chromatograms http://purl.obolibrary.org/obo/MS_4000003 single value The number of chromatograms recorded for the run. http://purl.obolibrary.org/obo/MS_4000072 observed mass accuracy http://purl.obolibrary.org/obo/MS_4000003 single value Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum. http://purl.obolibrary.org/obo/MS_4000073 QC sample metric http://purl.obolibrary.org/obo/MS_4000007 QC metric category A QC metric based on a QC sample of known content. http://purl.obolibrary.org/obo/MS_4000074 high complexity QC sample metric http://purl.obolibrary.org/obo/MS_4000073 QC sample metric A QC metric based on a QC sample of known and high complexity content. http://purl.obolibrary.org/obo/MS_4000075 low complexity QC sample metric http://purl.obolibrary.org/obo/MS_4000073 QC sample metric A QC metric based on a QC sample of known and low complexity content. http://purl.obolibrary.org/obo/MS_4000076 QC2 sample metric http://purl.obolibrary.org/obo/MS_4000074 high complexity QC sample metric A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design. http://purl.obolibrary.org/obo/MS_4000077 QC1 sample metric http://purl.obolibrary.org/obo/MS_4000075 low complexity QC sample metric A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design). http://purl.obolibrary.org/obo/MS_4000078 QC2 sample mass accuracies http://purl.obolibrary.org/obo/MS_4000005 table Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected. http://purl.obolibrary.org/obo/MS_4000079 QC2 sample intensities http://purl.obolibrary.org/obo/MS_4000005 table Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected. http://purl.obolibrary.org/obo/MS_4000081 first principal component http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term Data from the first principal component of a PCA. http://purl.obolibrary.org/obo/MS_4000082 second principal component http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term Data from the second principal component of a PCA. http://purl.obolibrary.org/obo/MS_4000083 third principal component http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term Data from the third principal component of a PCA. http://purl.obolibrary.org/obo/MS_4000084 fourth principal component http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term Data from the fourth principal component of a PCA. http://purl.obolibrary.org/obo/MS_4000085 fifth principal component http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term Data from the fifth principal component of a PCA. http://purl.obolibrary.org/obo/MS_4000086 mzQC input reference http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels. http://purl.obolibrary.org/obo/MS_4000087 mzQC plot label http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term Used to supply alternative labels for plotting figures. http://purl.obolibrary.org/obo/MS_4000088 batch label http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term Used to supply batch label information with any string value. http://purl.obolibrary.org/obo/MS_4000089 injection sequence label http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term Used to supply injection sequence information with consecutive whole numbers. http://purl.obolibrary.org/obo/MS_4000090 principal component analysis of MaxQuant's protein group raw intensities http://purl.obolibrary.org/obo/MS_4000005 table A table with the PCA results of MaxQuant's protein group raw intensities. http://purl.obolibrary.org/obo/MS_4000091 principal component analysis of MaxQuant's protein group lfq intensities http://purl.obolibrary.org/obo/MS_4000005 table A table with the PCA results of MaxQuant's protein group lfq intensities. http://purl.obolibrary.org/obo/MS_4000092 identified MS1 feature area principal component analysis result http://purl.obolibrary.org/obo/MS_4000005 table A table with the PCA results of identified MS1 feature areas. http://purl.obolibrary.org/obo/MS_4000093 unidentified MS1 feature area principal component analysis result http://purl.obolibrary.org/obo/MS_4000005 table A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas. http://purl.obolibrary.org/obo/MS_4000094 batch-corrected identified MS1 feature area principal component analysis result http://purl.obolibrary.org/obo/MS_4000005 table A table with the PCA results of identified MS1 feature areas after batch-correction. http://purl.obolibrary.org/obo/MS_1003369 average mass deisotoping http://purl.obolibrary.org/obo/MS_1000033 deisotoping The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution. http://purl.obolibrary.org/obo/MS_1002715 temperature chromatogram http://purl.obolibrary.org/obo/MS_1000626 chromatogram type Representation of temperature versus time. http://purl.obolibrary.org/obo/MS_1001102 SEQUEST:Chromatogram http://purl.obolibrary.org/obo/MS_1001006 SEQUEST:ViewCV http://purl.obolibrary.org/obo/MS_1001103 SEQUEST:InfoAndLog http://purl.obolibrary.org/obo/MS_1001006 SEQUEST:ViewCV http://purl.obolibrary.org/obo/MS_1001091 NoEnzyme http://purl.obolibrary.org/obo/MS_1001045 cleavage agent name http://purl.obolibrary.org/obo/MS_1001152 param: y ion-H2O DEPRECATED http://purl.obolibrary.org/obo/MS_1001066 ions series considered in search http://purl.obolibrary.org/obo/MS_1001147 protein ambiguity group result details http://purl.obolibrary.org/obo/MS_1001153 search engine specific score http://purl.obolibrary.org/obo/MS_1001095 SEQUEST:ProcessAll http://purl.obolibrary.org/obo/MS_1001087 SEQUEST:ProcessCV http://purl.obolibrary.org/obo/MS_1001111 SEQUEST:Full http://purl.obolibrary.org/obo/MS_1001110 SEQUEST:modeCV http://purl.obolibrary.org/obo/MS_1001120 SEQUEST:FormatAndLinks http://purl.obolibrary.org/obo/MS_1001110 SEQUEST:modeCV http://purl.obolibrary.org/obo/MS_1001126 SEQUEST:Fast http://purl.obolibrary.org/obo/MS_1001110 SEQUEST:modeCV http://purl.obolibrary.org/obo/MS_1001144 SEQUEST:SelectDefault http://purl.obolibrary.org/obo/MS_1001128 SEQUEST:selectCV http://purl.obolibrary.org/obo/MS_1001412 search tolerance plus value http://purl.obolibrary.org/obo/MS_1001411 search tolerance specification http://purl.obolibrary.org/obo/MS_1001413 search tolerance minus value http://purl.obolibrary.org/obo/MS_1001411 search tolerance specification http://purl.obolibrary.org/obo/MS_1001005 SEQUEST:CleavesAt http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter http://purl.obolibrary.org/obo/MS_1001026 SEQUEST:NormalizeXCorrValues http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter http://purl.obolibrary.org/obo/MS_1001032 SEQUEST:SequencePartialFilter http://purl.obolibrary.org/obo/MS_1002096 SEQUEST input parameter http://purl.obolibrary.org/obo/MS_1001433 ProteinExtractor:MascotUseIdentityScore http://purl.obolibrary.org/obo/MS_1002098 ProteinExtractor input parameter http://purl.obolibrary.org/obo/MS_1001158 SEQUEST:Uniq http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins http://purl.obolibrary.org/obo/MS_1001372 SEQUEST:Sequences http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins http://purl.obolibrary.org/obo/MS_1001374 SEQUEST:Sum http://purl.obolibrary.org/obo/MS_1002363 search engine specific score for proteins http://purl.obolibrary.org/obo/MS_0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies Proteomics Standards Initiative Mass Spectrometry Vocabularies. http://purl.obolibrary.org/obo/MS_1000007 inlet type The nature of the sample inlet. http://purl.obolibrary.org/obo/MS_1000008 ionization type The method by which gas phase ions are generated from the sample. http://purl.obolibrary.org/obo/MS_1000009 ionization mode OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer. http://purl.obolibrary.org/obo/MS_1000010 analyzer type OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted. http://purl.obolibrary.org/obo/MS_1000013 resolution type OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z. http://purl.obolibrary.org/obo/MS_1000017 Scan Function OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum. http://purl.obolibrary.org/obo/MS_1000018 scan direction Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low). http://purl.obolibrary.org/obo/MS_1000019 scan law Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used. http://purl.obolibrary.org/obo/MS_1000020 scanning method Describes the acquisition data type produced by a tandem mass spectrometry experiment. http://purl.obolibrary.org/obo/MS_1000023 isolation width OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion. http://purl.obolibrary.org/obo/MS_1000026 detector type Type of detector used in the mass spectrometer. http://purl.obolibrary.org/obo/MS_1000027 detector acquisition mode Method by which detector signal is acquired by the data system. http://purl.obolibrary.org/obo/MS_1000030 vendor OBSOLETE Name of instrument vendor. http://purl.obolibrary.org/obo/MS_1000031 instrument model Instrument model name not including the vendor's name. http://purl.obolibrary.org/obo/MS_1000036 scan mode OBSOLETE. http://purl.obolibrary.org/obo/MS_1000037 polarity OBSOLETE Terms to describe the polarity setting of the instrument. http://purl.obolibrary.org/obo/MS_1000038 minute OBSOLETE Acquisition time in minutes. http://purl.obolibrary.org/obo/MS_1000039 second OBSOLETE Acquisition time in seconds. http://purl.obolibrary.org/obo/MS_1000044 dissociation method Fragmentation method used for dissociation or fragmentation. http://purl.obolibrary.org/obo/MS_1000054 chromatography OBSOLETE Chromatographic conditions used to obtain the sample. http://purl.obolibrary.org/obo/MS_1000072 Electronic Ionization OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. http://purl.obolibrary.org/obo/MS_1000088 constant OBSOLETE When resolution is constant with respect to m/z. http://purl.obolibrary.org/obo/MS_1000089 proportional OBSOLETE When resolution is proportional with respect to m/z. http://purl.obolibrary.org/obo/MS_1000090 mass scan OBSOLETE A variation of instrument where a selected mass is scanned. http://purl.obolibrary.org/obo/MS_1000091 selected ion detection OBSOLETE Please see Single Ion Monitoring. http://purl.obolibrary.org/obo/MS_1000097 constant neutral mass loss OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. http://purl.obolibrary.org/obo/MS_1000098 multiple ion monitoring OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring. http://purl.obolibrary.org/obo/MS_1000099 multiple reaction monitoring OBSOLETE This term is not recommended. See Selected Reaction Monitoring. http://purl.obolibrary.org/obo/MS_1000100 precursor ion scan OBSOLETE The specific scan function or process that will record a precursor ion spectrum. http://purl.obolibrary.org/obo/MS_1000101 product ion scan OBSOLETE The specific scan function or process that records product ion spectrum. http://purl.obolibrary.org/obo/MS_1000102 single ion monitoring OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum. http://purl.obolibrary.org/obo/MS_1000103 single reaction monitoring OBSOLETE This term is not recommended. See Selected Reaction Monitoring. http://purl.obolibrary.org/obo/MS_1000104 None ?? OBSOLETE None. http://purl.obolibrary.org/obo/MS_1000137 electron volt OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J. http://purl.obolibrary.org/obo/MS_1000155 ELEMENT2 OBSOLETE ThermoFinnigan ELEMENT2 MS. http://purl.obolibrary.org/obo/MS_1000207 accurate mass OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition. http://purl.obolibrary.org/obo/MS_1000208 average mass OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance. http://purl.obolibrary.org/obo/MS_1000209 appearance energy OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended. http://purl.obolibrary.org/obo/MS_1000211 OBSOLETE charge number OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state. http://purl.obolibrary.org/obo/MS_1000212 dalton OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg. http://purl.obolibrary.org/obo/MS_1000213 electron affinity OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy. http://purl.obolibrary.org/obo/MS_1000214 electron energy obsolete OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization. http://purl.obolibrary.org/obo/MS_1000215 exact mass OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom. http://purl.obolibrary.org/obo/MS_1000217 ionization cross section OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule. http://purl.obolibrary.org/obo/MS_1000218 ionization efficiency OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used. http://purl.obolibrary.org/obo/MS_1000219 ionization energy OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion. http://purl.obolibrary.org/obo/MS_1000220 isotope dilution mass spectrometry OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard. http://purl.obolibrary.org/obo/MS_1000222 mass defect OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom. http://purl.obolibrary.org/obo/MS_1000223 mass number OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion. http://purl.obolibrary.org/obo/MS_1000225 monoisotopic mass OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element. http://purl.obolibrary.org/obo/MS_1000226 molecular beam mass spectrometry OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam. http://purl.obolibrary.org/obo/MS_1000228 nitrogen rule OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms. http://purl.obolibrary.org/obo/MS_1000229 nominal mass OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value. http://purl.obolibrary.org/obo/MS_1000230 odd-electron rule OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions. http://purl.obolibrary.org/obo/MS_1000231 peak A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably. http://purl.obolibrary.org/obo/MS_1000232 peak intensity OBSOLETE The height or area of a peak in a mass spectrum. http://purl.obolibrary.org/obo/MS_1000233 proton affinity OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states. http://purl.obolibrary.org/obo/MS_1000234 mass resolving power OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported. http://purl.obolibrary.org/obo/MS_1000237 unified atomic mass unit OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg. http://purl.obolibrary.org/obo/MS_1000238 accelerator mass spectrometry OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy. http://purl.obolibrary.org/obo/MS_1000241 Atmostpheric Pressure Photoionization OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. http://purl.obolibrary.org/obo/MS_1000243 charge-remote fragmentation OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site. http://purl.obolibrary.org/obo/MS_1000244 consecutive reaction monitoring OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. http://purl.obolibrary.org/obo/MS_1000251 even-electron ion OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state. http://purl.obolibrary.org/obo/MS_1000252 electron-induced excitation in organics OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion. http://purl.obolibrary.org/obo/MS_1000256 high-field asymmetric waveform ion mobility spectrometry OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion. http://purl.obolibrary.org/obo/MS_1000260 ion kinetic energy spectrometry OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge. http://purl.obolibrary.org/obo/MS_1000261 ion mobility spectrometry OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field. http://purl.obolibrary.org/obo/MS_1000263 isotope ratio mass spectrometry OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer. http://purl.obolibrary.org/obo/MS_1000265 kinetic energy release distribution OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction. http://purl.obolibrary.org/obo/MS_1000266 Laser Desorption OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules. http://purl.obolibrary.org/obo/MS_1000267 mass analyzed ion kinetic energy spectrometry OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process. http://purl.obolibrary.org/obo/MS_1000268 mass spectrometry OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments. http://purl.obolibrary.org/obo/MS_1000269 mass spectrometry/mass spectrometry OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions. http://purl.obolibrary.org/obo/MS_1000270 multiple stage mass spectrometry OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions. http://purl.obolibrary.org/obo/MS_1000277 residual gas analyzer OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber. http://purl.obolibrary.org/obo/MS_1000280 surface ionization OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. http://purl.obolibrary.org/obo/MS_1000283 Spark Source Mass Spectrometry OBSOLETE Mass spectrometry using spark ionization. http://purl.obolibrary.org/obo/MS_1000287 time-of-flight mass spectrometer OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy. http://purl.obolibrary.org/obo/MS_1000289 double-focusing mass spectrometer OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam. http://purl.obolibrary.org/obo/MS_1000290 hybrid mass spectrometer OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry. http://purl.obolibrary.org/obo/MS_1000292 mass spectrograph obsolete OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate. http://purl.obolibrary.org/obo/MS_1000293 mass spectrometer OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions. http://purl.obolibrary.org/obo/MS_1000295 mattauch-herzog geometry OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians. http://purl.obolibrary.org/obo/MS_1000296 nier-johnson geometry OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians. http://purl.obolibrary.org/obo/MS_1000297 paul ion trap OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected. http://purl.obolibrary.org/obo/MS_1000298 prolate traochoidal mass spectrometer OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path. http://purl.obolibrary.org/obo/MS_1000299 quistor OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term. http://purl.obolibrary.org/obo/MS_1000301 sector mass spectrometer OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection. http://purl.obolibrary.org/obo/MS_1000302 tandem mass spectrometer OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry. http://purl.obolibrary.org/obo/MS_1000303 transmission quadrupole mass spectrometer OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. http://purl.obolibrary.org/obo/MS_1000305 cyclotron motion OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB. http://purl.obolibrary.org/obo/MS_1000306 dynamic mass spectrometry OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time. http://purl.obolibrary.org/obo/MS_1000312 mass limit OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer. http://purl.obolibrary.org/obo/MS_1000313 scan m/z range? OBSOLETE The limit of m/z over which a mass spectrometer can detect ions. http://purl.obolibrary.org/obo/MS_1000314 mass selective axial ejection OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap. http://purl.obolibrary.org/obo/MS_1000315 mass selective instability OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap. http://purl.obolibrary.org/obo/MS_1000316 mathieu stability diagram OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer. http://purl.obolibrary.org/obo/MS_1000317 orthogonal extraction OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage. http://purl.obolibrary.org/obo/MS_1000318 resonance ion ejection OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it. http://purl.obolibrary.org/obo/MS_1000321 2E Mass Spectrum OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained. http://purl.obolibrary.org/obo/MS_1000323 constant neutral loss scan OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement. http://purl.obolibrary.org/obo/MS_1000324 constant neutral gain scan OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment. http://purl.obolibrary.org/obo/MS_1000327 consecutive reaction monitoring OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. http://purl.obolibrary.org/obo/MS_1000329 linked scan OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum. http://purl.obolibrary.org/obo/MS_1000330 linked scan at constant b/e OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. http://purl.obolibrary.org/obo/MS_1000331 Linked Scan at Constant E2/V OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan records a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors. http://purl.obolibrary.org/obo/MS_1000332 Linked Scan at Constant B2/E OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended. http://purl.obolibrary.org/obo/MS_1000333 Linked Scan at Constant B[1-(E/E0)]^1/2 / E OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan. http://purl.obolibrary.org/obo/MS_1000334 MS/MS in Time OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discrete steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time. http://purl.obolibrary.org/obo/MS_1000335 MS/MS in Space OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition. http://purl.obolibrary.org/obo/MS_1000337 nth generation product ion OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated. http://purl.obolibrary.org/obo/MS_1000338 nth generation product ion scan OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions. http://purl.obolibrary.org/obo/MS_1000339 nth generation product ion spectrum OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions. http://purl.obolibrary.org/obo/MS_1000340 precursor ion OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated. http://purl.obolibrary.org/obo/MS_1000342 product ion OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated. http://purl.obolibrary.org/obo/MS_1000344 progeny ion OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+. http://purl.obolibrary.org/obo/MS_1000352 secondary electron OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go. http://purl.obolibrary.org/obo/MS_1000354 aromatic ion OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure. http://purl.obolibrary.org/obo/MS_1000355 analog ion OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+. http://purl.obolibrary.org/obo/MS_1000356 anti-aromatic ion OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic. http://purl.obolibrary.org/obo/MS_1000357 cationized molecule OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used. http://purl.obolibrary.org/obo/MS_1000358 cluster ion OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-. http://purl.obolibrary.org/obo/MS_1000359 Conventional ion OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion. http://purl.obolibrary.org/obo/MS_1000360 diagnostic ion OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives. http://purl.obolibrary.org/obo/MS_1000361 dimeric ion OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+. http://purl.obolibrary.org/obo/MS_1000362 distonic ion OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion. http://purl.obolibrary.org/obo/MS_1000363 enium ion OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions. http://purl.obolibrary.org/obo/MS_1000364 fragment ion OBSOLETE A product ion that results from the dissociation of a precursor ion. http://purl.obolibrary.org/obo/MS_1000365 ion? OBSOLETE An atomic or molecular species having a net positive or negative electric charge. http://purl.obolibrary.org/obo/MS_1000366 Isotopologue ion OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue. http://purl.obolibrary.org/obo/MS_1000367 Isotopomeric ion OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer. http://purl.obolibrary.org/obo/MS_1000368 metastable ion OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection. http://purl.obolibrary.org/obo/MS_1000369 molecular ion OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion. http://purl.obolibrary.org/obo/MS_1000370 negative ion OBSOLETE An atomic or molecular species having a net negative electric charge. http://purl.obolibrary.org/obo/MS_1000371 non-classical ion OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions. http://purl.obolibrary.org/obo/MS_1000372 onium ion OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+. http://purl.obolibrary.org/obo/MS_1000373 principal ion OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions. http://purl.obolibrary.org/obo/MS_1000374 positive ion OBSOLETE An atomic or molecular species having a net positive electric charge. http://purl.obolibrary.org/obo/MS_1000375 protonated molecule OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended. http://purl.obolibrary.org/obo/MS_1000376 radical ion OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation. http://purl.obolibrary.org/obo/MS_1000377 reference ion OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion. http://purl.obolibrary.org/obo/MS_1000378 stable ion OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer. http://purl.obolibrary.org/obo/MS_1000379 unstable ion OBSOLETE An ion with sufficient energy to dissociate within the ion source. http://purl.obolibrary.org/obo/MS_1000390 ion desolvation OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules. http://purl.obolibrary.org/obo/MS_1000391 ion-pair formation OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products. http://purl.obolibrary.org/obo/MS_1000401 pre-ionization state OBSOLETE An electronic state capable of undergoing auto-Ionization. http://purl.obolibrary.org/obo/MS_1000409 association reaction OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion. http://purl.obolibrary.org/obo/MS_1000410 alpha-cleavage OBSOLETE A homolytic cleavage where the bond fission occurs between the atom adjacent to the atom at the apparent charge site and an atom removed from the apparent charge site by two bonds. http://purl.obolibrary.org/obo/MS_1000411 beta-cleavage OBSOLETE A homolytic cleavage where the bond fission occurs between an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the apparent charge site by three bonds. http://purl.obolibrary.org/obo/MS_1000413 charge-induced fragmentation OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation. http://purl.obolibrary.org/obo/MS_1000414 charge inversion reaction OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion. http://purl.obolibrary.org/obo/MS_1000415 charge permutation reaction OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion. http://purl.obolibrary.org/obo/MS_1000416 charge stripping reaction OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion. http://purl.obolibrary.org/obo/MS_1000417 charge transfer reaction OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species. http://purl.obolibrary.org/obo/MS_1000418 collisional excitation OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion. http://purl.obolibrary.org/obo/MS_1000420 heterolytic cleavage OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis. http://purl.obolibrary.org/obo/MS_1000421 high energy collision OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV. http://purl.obolibrary.org/obo/MS_1000423 homolytic cleavage OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis. http://purl.obolibrary.org/obo/MS_1000424 hydrogen/deuterium exchange OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer. http://purl.obolibrary.org/obo/MS_1000425 ion energy loss spectrum OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species. http://purl.obolibrary.org/obo/MS_1000426 ionizing collision OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral. http://purl.obolibrary.org/obo/MS_1000427 ion/molecule reaction OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule. http://purl.obolibrary.org/obo/MS_1000428 ion/neutral complex OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions. http://purl.obolibrary.org/obo/MS_1000429 ion/neutral species reaction OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants. http://purl.obolibrary.org/obo/MS_1000430 ion/neutral species exchange reaction OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product. http://purl.obolibrary.org/obo/MS_1000431 kinetic method OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account. http://purl.obolibrary.org/obo/MS_1000432 low energy collisions OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower. http://purl.obolibrary.org/obo/MS_1000434 McLafferty Rearrangement OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied. http://purl.obolibrary.org/obo/MS_1000436 partial charge transfer reaction OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral. http://purl.obolibrary.org/obo/MS_1000437 ion reaction OBSOLETE Chemical transformation involving an ion. http://purl.obolibrary.org/obo/MS_1000438 superelastic collision OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners. http://purl.obolibrary.org/obo/MS_1000439 surface-induced reaction OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion. http://purl.obolibrary.org/obo/MS_1000440 unimolecular dissociation OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion. http://purl.obolibrary.org/obo/MS_1000441 scan Function or process of the mass spectrometer where it records a spectrum. http://purl.obolibrary.org/obo/MS_1000442 spectrum Representation of intensity values corresponding to a range of measurement space. http://purl.obolibrary.org/obo/MS_1000443 mass analyzer type Mass analyzer separates the ions according to their mass-to-charge ratio. http://purl.obolibrary.org/obo/MS_1000444 m/z Separation Method OBSOLETE Mass/charge separation Method. http://purl.obolibrary.org/obo/MS_1000445 sequential m/z separation method OBSOLETE Sequential m/z separation method. http://purl.obolibrary.org/obo/MS_1000451 mass analyzer Terms used to describe the Analyzer. http://purl.obolibrary.org/obo/MS_1000452 data transformation Terms used to describe types of data processing. http://purl.obolibrary.org/obo/MS_1000453 detector The device that detects ions. http://purl.obolibrary.org/obo/MS_1000454 instrument additional description OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5. http://purl.obolibrary.org/obo/MS_1000456 precursor activation Terms to describe the precursor activation. http://purl.obolibrary.org/obo/MS_1000457 sample Terms to describe the sample. http://purl.obolibrary.org/obo/MS_1000458 source Terms to describe the source. http://purl.obolibrary.org/obo/MS_1000459 spectrum instrument description OBSOLETE Terms used to describe the spectrum. http://purl.obolibrary.org/obo/MS_1000460 unit OBSOLETE Terms to describe units. http://purl.obolibrary.org/obo/MS_1000461 additional description OBSOLETE Terms to describe Additional. http://purl.obolibrary.org/obo/MS_1000462 ion optics Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions. http://purl.obolibrary.org/obo/MS_1000463 instrument Description of the instrument or the mass spectrometer. http://purl.obolibrary.org/obo/MS_1000464 mass unit OBSOLETE A unit of measurement for mass. http://purl.obolibrary.org/obo/MS_1000465 scan polarity Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer. http://purl.obolibrary.org/obo/MS_1000466 alternating OBSOLETE Alternating. http://purl.obolibrary.org/obo/MS_1000479 purgatory OBSOLETE Terms that will likely become obsolete unless there are wails of dissent. http://purl.obolibrary.org/obo/MS_1000480 mass analyzer attribute Analyzer properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1000481 detector attribute Detector attribute recognized as a value. http://purl.obolibrary.org/obo/MS_1000482 source attribute Property of a source device that need a value. http://purl.obolibrary.org/obo/MS_1000498 full scan OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range. http://purl.obolibrary.org/obo/MS_1000499 spectrum attribute Nonphysical characteristic attributed to a spectrum. http://purl.obolibrary.org/obo/MS_1000506 ion role OBSOLETE Ion Role. http://purl.obolibrary.org/obo/MS_1000507 ion property Nonphysical characteristic attributed to an ion. http://purl.obolibrary.org/obo/MS_1000508 ion chemical type OBSOLETE Ion Type. http://purl.obolibrary.org/obo/MS_1000510 precursor activation attribute Precursor Activation Attribute. http://purl.obolibrary.org/obo/MS_1000513 binary data array A data array of values. http://purl.obolibrary.org/obo/MS_1000518 binary data type Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float. http://purl.obolibrary.org/obo/MS_1000524 data file content Describes the data content on the file. http://purl.obolibrary.org/obo/MS_1000525 spectrum representation Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks. http://purl.obolibrary.org/obo/MS_1000531 software Software related to the recording or transformation of spectra. http://purl.obolibrary.org/obo/MS_1000547 object attribute Object Attribute. http://purl.obolibrary.org/obo/MS_1000550 time unit OBSOLETE Time Unit. http://purl.obolibrary.org/obo/MS_1000552 maldi spot identifier OBSOLETE Maldi Spot Identifier. http://purl.obolibrary.org/obo/MS_1000559 spectrum type Spectrum type. http://purl.obolibrary.org/obo/MS_1000561 data file checksum type Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data. http://purl.obolibrary.org/obo/MS_1000570 spectra combination Method used to combine the mass spectra. http://purl.obolibrary.org/obo/MS_1000572 binary data compression type Compression Type. http://purl.obolibrary.org/obo/MS_1000596 measurement method An attribute of resolution when recording the detector response in absence of the analyte. http://purl.obolibrary.org/obo/MS_1000625 chromatogram Representation of a chromatographic separation attribute measurement versus time. http://purl.obolibrary.org/obo/MS_1000626 chromatogram type Type of chromatogram measurement being represented. http://purl.obolibrary.org/obo/MS_1000630 data processing parameter Data processing parameter used in the data processing performed on the data file. http://purl.obolibrary.org/obo/MS_1000767 native spectrum identifier format Describes how the native spectrum identifiers are formatted. http://purl.obolibrary.org/obo/MS_1000791 enhanced resolution scan OBSOLETE Scan with enhanced resolution. http://purl.obolibrary.org/obo/MS_1000832 MALDI matrix application Attributes to describe the technique how the sample is prepared with the matrix solution. http://purl.obolibrary.org/obo/MS_1000833 matrix application type Describes the technique how the matrix is put on the sample target. http://purl.obolibrary.org/obo/MS_1000840 laser Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation. http://purl.obolibrary.org/obo/MS_1000841 laser attribute Laser properties that are associated with a value. http://purl.obolibrary.org/obo/MS_1000842 laser type Type of laser used for desorption purpose. http://purl.obolibrary.org/obo/MS_1000861 molecular entity property A physical characteristic of a molecular entity. http://purl.obolibrary.org/obo/MS_1000881 molecular entity Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. http://purl.obolibrary.org/obo/MS_1000887 peptide attribute Nonphysical characteristic attributed to a peptide. http://purl.obolibrary.org/obo/MS_1000898 standard Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence. http://purl.obolibrary.org/obo/MS_1000908 transition A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely. http://purl.obolibrary.org/obo/MS_1000909 transition validation method The strategy used to validate that a transition is effective. http://purl.obolibrary.org/obo/MS_1000915 retention time window attribute An attribute of a window in time about which a peptide might elute from the column. http://purl.obolibrary.org/obo/MS_1000918 target list A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically. http://purl.obolibrary.org/obo/MS_1000919 target inclusion exclusion priority A priority setting specifying whether included or excluded targets have priority over the other. http://purl.obolibrary.org/obo/MS_1000924 MaRiMba OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. http://purl.obolibrary.org/obo/MS_1001000 spectrum interpretation Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra. http://purl.obolibrary.org/obo/MS_1001051 multiple enzyme combination rules OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any. http://purl.obolibrary.org/obo/MS_1001055 modification parameters Modification parameters for the search engine run. http://purl.obolibrary.org/obo/MS_1001115 scan number(s) OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData. http://purl.obolibrary.org/obo/MS_1001129 quantification information Quantification information. http://purl.obolibrary.org/obo/MS_1001213 search result details OBSOLETE: Scores and global result characteristics. http://purl.obolibrary.org/obo/MS_1001249 search input details Details describing the search input. http://purl.obolibrary.org/obo/MS_1001291 decoy DB from nr OBSOLETE Decoy database from a non-redundant GenBank sequence database. http://purl.obolibrary.org/obo/MS_1001292 decoy DB from IPI_rat OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus. http://purl.obolibrary.org/obo/MS_1001293 decoy DB from IPI_mouse OBSOLETE Decoy database from a International Protein Index database for Mus musculus. http://purl.obolibrary.org/obo/MS_1001294 decoy DB from IPI_arabidopsis OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana. http://purl.obolibrary.org/obo/MS_1001295 decoy DB from EST OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database. http://purl.obolibrary.org/obo/MS_1001296 decoy DB from IPI_zebrafish OBSOLETE Decoy database from a International Protein Index database for Danio rerio. http://purl.obolibrary.org/obo/MS_1001297 decoy DB from UniProtKB/Swiss-Prot OBSOLETE Decoy database from a Swiss-Prot protein sequence database. http://purl.obolibrary.org/obo/MS_1001298 decoy DB from IPI_chicken OBSOLETE Decoy database from a International Protein Index database for Gallus gallus. http://purl.obolibrary.org/obo/MS_1001299 decoy DB from IPI_cow OBSOLETE Decoy database from a International Protein Index database for Bos taurus. http://purl.obolibrary.org/obo/MS_1001300 decoy DB from IPI_human OBSOLETE Decoy database from a International Protein Index database for Homo sapiens. http://purl.obolibrary.org/obo/MS_1001326 add_others OBSOLETE. http://purl.obolibrary.org/obo/MS_1001354 mass table options Root node for options for the mass table used. http://purl.obolibrary.org/obo/MS_1001359 ambiguous residues Children of this term describe ambiguous residues. http://purl.obolibrary.org/obo/MS_1001405 spectrum identification result details This subsection describes terms which can describe details of spectrum identification results. http://purl.obolibrary.org/obo/MS_1001458 spectrum generation information Vocabularies describing the spectrum generation information. http://purl.obolibrary.org/obo/MS_1001459 file format Format of data files. http://purl.obolibrary.org/obo/MS_1001471 peptide modification details The children of this term can be used to describe modifications. http://purl.obolibrary.org/obo/MS_1001797 travelling wave ion mobility mass spectrometer OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide. http://purl.obolibrary.org/obo/MS_1001861 quantification data processing Terms used to describe types of quantification data processing. http://purl.obolibrary.org/obo/MS_1001882 transition validation attribute Attributes of the quality of a transition that affect its selection as appropriate. http://purl.obolibrary.org/obo/MS_1001931 source interface The source interface. http://purl.obolibrary.org/obo/MS_1001932 source interface model The source interface model. http://purl.obolibrary.org/obo/MS_1001933 source sprayer The source sprayer. http://purl.obolibrary.org/obo/MS_1001934 source sprayer type The source sprayer type. http://purl.obolibrary.org/obo/MS_1001935 source sprayer manufacturer The source sprayer manufacturer. http://purl.obolibrary.org/obo/MS_1001936 source sprayer model The source sprayer model. http://purl.obolibrary.org/obo/MS_1001937 sample plate Plate where the sample solution is spotted in a MALDI or similar instrument. http://purl.obolibrary.org/obo/MS_1001938 sample plate type The sample plate type. http://purl.obolibrary.org/obo/MS_1001941 electrospray supply type Whether the sprayer is fed or is loaded with sample once. http://purl.obolibrary.org/obo/MS_1001953 source interface manufacturer The source interface manufacturer. http://purl.obolibrary.org/obo/MS_1001954 acquisition parameter Parameters used in the mass spectrometry acquisition. http://purl.obolibrary.org/obo/MS_1001961 peptide spectrum match scoring algorithm Algorithm used to score the match between a spectrum and a peptide ion. http://purl.obolibrary.org/obo/MS_1002006 SRM transition type The type of the transitions, e.g. target or decoy. http://purl.obolibrary.org/obo/MS_1002061 decoy DB from UniProtKB/TrEMBL OBSOLETE Decoy database from a TrEMBL protein sequence database. http://purl.obolibrary.org/obo/MS_1002108 higher score better Indicates that a higher score is better. http://purl.obolibrary.org/obo/MS_1002109 lower score better Indicates that a lower score is better. http://purl.obolibrary.org/obo/MS_1002304 domain range Domain range of a numerical value. http://purl.obolibrary.org/obo/MS_1002343 ion stability type OBSOLETE Stability type of the ion. http://purl.obolibrary.org/obo/MS_1002438 spectrum identification list result details Information about the list of PSMs (SpectrumIdentificationList). http://purl.obolibrary.org/obo/MS_1002479 regular expression Regular expression. http://purl.obolibrary.org/obo/MS_1002646 native spectrum identifier format, combined spectra Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formatted. http://purl.obolibrary.org/obo/MS_1002658 identification parameter Identification parameter for the search engine run. http://purl.obolibrary.org/obo/MS_1002675 crosslinking result details This subsection describes terms which can describe details of crosslinking results. http://purl.obolibrary.org/obo/MS_1003300 spectrum match Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte. http://purl.obolibrary.org/obo/MS_1003298 contributing replicate spectrum keys A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys. http://purl.obolibrary.org/obo/MS_1003348 proteomics large-scale study of proteins and proteomes. http://purl.obolibrary.org/obo/MS_1003372 specification document extension version The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file. http://purl.obolibrary.org/obo/NCIT_C43431 Activity An active process; excludes processes and mechanisms which fulfill biological functions. http://purl.obolibrary.org/obo/MS_1003737 separation system A system to effect separation of compounds. http://purl.obolibrary.org/obo/PEFF_0000001 PEFF CV term PSI Extended FASTA Format controlled vocabulary term. http://purl.obolibrary.org/obo/MS_1003271 peak annotation The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum. http://purl.obolibrary.org/obo/MS_1003272 peak annotation string A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'. http://purl.obolibrary.org/obo/MS_1003273 peak annotation confidence A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'. http://purl.obolibrary.org/obo/MS_1003212 library attribute set name A name to refer to a library attribute set http://purl.obolibrary.org/obo/MS_4000000 PSI-MS CV Quality Control Vocabulary PSI Quality Control controlled vocabulary term. http://purl.obolibrary.org/obo/MS_4000001 QC metric Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations. http://purl.obolibrary.org/obo/MS_4000002 QC metric value type The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix. http://purl.obolibrary.org/obo/MS_4000007 QC metric category Categorization of the QC metric. http://purl.obolibrary.org/obo/UO_0000000 unit A unit of measurement is a standardized quantity of a physical quality. http://purl.obolibrary.org/obo/NCIT_C20181 Conceptual Entity An organizational header for concepts representing mostly abstract entities. http://purl.obolibrary.org/obo/MS_1003299 contributing replicate spectrum USI A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers. http://purl.obolibrary.org/obo/MS_1003761 instrument class Instruments classified based on their architecture with respect to mass analyzers. http://purl.obolibrary.org/obo/MS_1002709 compound data type A data type representing more than a single value. http://purl.obolibrary.org/obo/MS_1003091 binary data compression parameter Settable parameter for a binary data compression event. http://purl.obolibrary.org/obo/MS_1003170 spectral library A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments http://purl.obolibrary.org/obo/MS_1003171 spectral library attribute An attribute of a spectral library http://purl.obolibrary.org/obo/MS_1003172 library spectrum An entry in a spectral library representing a spectrum http://purl.obolibrary.org/obo/MS_1003174 attribute maximum The maximum value for this attribute http://purl.obolibrary.org/obo/MS_1003175 attribute minimum The minimum value for this attribute http://purl.obolibrary.org/obo/MS_1003176 attribute mean The arithmetic mean value for this attribute http://purl.obolibrary.org/obo/MS_1003177 attribute standard deviation The standard deviation (exact value of population, or estimate from sample) of this attribute http://purl.obolibrary.org/obo/MS_1003178 attribute coefficient of variation The coefficient of variation of this attribute, i.e. standard deviation divided by the mean http://purl.obolibrary.org/obo/MS_1003179 attribute summary value The most appropriate summary value of the attribute, usually but not necessarily the mean http://purl.obolibrary.org/obo/MS_1003180 attribute median The median of this attribute http://purl.obolibrary.org/obo/MS_1002809 adduct ion attribute Nonphysical characteristic attributed to an adduct ion. http://purl.obolibrary.org/obo/MS_1003033 molecular entity attribute Non-inherent characteristic attributed to a molecular entity. http://purl.obolibrary.org/obo/MS_1003050 peptidoform attribute Non-inherent characteristic attributed to a peptidoform. http://purl.obolibrary.org/obo/MS_1003052 peptidoform ion property Inherent or measurable characteristic of a peptidoform ion. http://purl.obolibrary.org/obo/MS_1003056 adduct ion property Physical measurable characteristic of an adduct ion. http://purl.obolibrary.org/obo/MS_1003058 spectrum property Inherent or measurable characteristic of a spectrum. http://purl.obolibrary.org/obo/MS_1003078 interpreted spectrum attribute Non-inherent characteristic attributed to an interpreted spectrum. http://purl.obolibrary.org/obo/NCIT_C20189 Property or Attribute A distinguishing quality or prominent aspect of a person, object, action, process, or substance. http://purl.obolibrary.org/obo/MS_1003903 analysis A strategy for mass spectrometry-based analysis that defines whether analytes are predetermined or discovered during acquisition. http://purl.obolibrary.org/obo/MS_1003234 library spectrum attribute An attribute that describes information about an entry in a spectral library http://purl.obolibrary.org/obo/MS_1002840 external reference data Data belonging to an external reference. http://purl.obolibrary.org/obo/MS_1003578 obsolete liquid chromatography OBSOLETE. The methods, technology and chemistry by which a liquid chromatography system effects the separation of compounds. http://purl.obolibrary.org/obo/MS_1003588 hyphenated separation system An on-line coupled system to effect separation of compounds prior to detection with a spectrometric or other detection technology. http://purl.obolibrary.org/obo/MS_1003025 named element A named element that is an attribute in a proteomics standards file. http://purl.obolibrary.org/obo/MS_1003254 peak attribute An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation. http://purl.obolibrary.org/obo/MS_1003256 peptidoform ion attribute Non-inherent characteristic attributed to a peptidoform http://purl.obolibrary.org/obo/MS_1003261 related spectrum description A free-text string describing the related spectrum and/or its relationship to this spectrum http://purl.obolibrary.org/obo/MS_1003265 spectrum cluster A group of spectra that are spectrally similar to each other http://purl.obolibrary.org/obo/MS_1003266 spectrum cluster attribute A non-inherent characteristic of a spectrum cluster http://purl.obolibrary.org/obo/MS_4000080 QC non-metric term QC terms associated but not directly metrics themselves. http://purl.obolibrary.org/obo/MS_1002716 measured element The component or dimension of an object being measured, for example the temperature of an instrument component over time. http://purl.obolibrary.org/obo/ms#has_value_type has value type 'Entity A' has value type 'Entity B', such as xsd:float. http://purl.obolibrary.org/obo/ms#has_structured_representation_in_format has structured representation in format The term is encoded in the structure of the named file format rather than as an explicit parameter, and should not be used as one in that format. http://purl.obolibrary.org/obo/ms#has_column has_column http://purl.obolibrary.org/obo/ms#has_metric_category has_metric_category http://purl.obolibrary.org/obo/ms#has_optional_column has_optional_column http://purl.obolibrary.org/obo/ms#has_value_concept has_value_concept http://purl.obolibrary.org/obo/ms#has_order has_order http://purl.obolibrary.org/obo/ms#has_domain has_domain http://purl.obolibrary.org/obo/ms#has_regexp has regexp http://purl.obolibrary.org/obo/ms#has_units has_units http://purl.obolibrary.org/obo/BFO_0000050 part_of