format-version: 1.2 date: 07:07:2008 14:30 saved-by: David Sparkman auto-generated-by: OBO-Edit 1.101 default-namespace: MS remark: namespace: MS remark: version: 1.12.0 remark: release date: 2008-12-17 remark: coverage: Mass spectrometer output files remark: creator: Fredrik Levander immun.lth.se> remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html. import: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo?revision=1.15 [Term] id: MS:0000000 name: Proteomics Standards Initiative Mass Spectrometry Ontology def: "Proteomics Standards Initiative Mass Spectrometry Ontology." [PSI:MS] [Term] id: MS:1000001 name: sample number def: "A reference number relevant to the sample under study." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute [Term] id: MS:1000002 name: sample name def: "A reference string relevant to the sample under study." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000003 name: sample state def: "The chemical phase of a pure sample, or the state of a mixed sample." [PSI:MS] is_a: MS:1000548 ! sample attribute [Term] id: MS:1000004 name: sample mass def: "Total mass of sample used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000002 ! mass unit [Term] id: MS:1000005 name: sample volume def: "Total volume of solution used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000095 ! volume unit [Term] id: MS:1000006 name: sample concentration def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000051 ! concentration unit [Term] id: MS:1000007 name: inlet type def: "The nature of the sample inlet." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1000008 name: ionization type def: "The method by which gas phase ions are generated from the sample." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1000009 name: ionization mode def: "Whether positive or negative ions are selected for analysis by the spectrometer. Re-map to Polarity Mode." [PSI:MS] is_obsolete: true [Term] id: MS:1000010 name: analyzer type def: "The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000011 name: mass resolution def: "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute [Term] id: MS:1000012 name: resolution measurement method def: "Which of the available standard measures is used to define whether two peaks are separate." [PSI:MS] is_a: MS:1000596 ! measurement method [Term] id: MS:1000013 name: resolution type def: "Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000014 name: accuracy def: "Accuracy is the degree of conformity of a measured mass to its actual value." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000480 ! mass analyzer attribute relationship: has_units UO:0000166 ! parts per notation [Term] id: MS:1000015 name: scan rate def: "Rate in (m/z)/sec for scanning analyzers." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute [Term] id: MS:1000016 name: scan time def: "The time that an analyzer started a scan, relative to the start of the run." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000003 ! time unit [Term] id: MS:1000017 name: Scan Function def: "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." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000018 name: scan direction def: "Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low)." [PSI:MS] relationship: part_of MS:1000441 ! scan [Term] id: MS:1000019 name: scan law def: "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." [PSI:MS] relationship: part_of MS:1000441 ! scan [Term] id: MS:1000020 name: scanning method def: "Describes the acquisition data type produced by a tandem mass spectrometry experiment." [PSI:MS] synonym: "Tandem Scanning Method" RELATED [] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000021 name: reflectron state def: "Status of the reflectron, turned on or off." [PSI:MS] is_a: MS:1000480 ! mass analyzer attribute [Term] id: MS:1000022 name: TOF Total Path Length def: "The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000480 ! mass analyzer attribute relationship: has_units UO:0000001 ! length unit [Term] id: MS:1000023 name: isolation width def: "The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000479 ! purgatory relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000024 name: final MS exponent def: "Final MS level achieved when performing PFF with the ion trap (e.g. MS E10)." [PSI:MS] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1000480 ! mass analyzer attribute [Term] id: MS:1000025 name: magnetic field strength def: "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." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." synonym: "B" EXACT [] synonym: "Magnetic Field" RELATED [] is_a: MS:1000480 ! mass analyzer attribute relationship: has_units UO:0000227 ! magnetic flux density [Term] id: MS:1000026 name: detector type def: "Type of detector used in the mass spectrometer." [PSI:MS] relationship: part_of MS:1000453 ! detector [Term] id: MS:1000027 name: detector acquisition mode def: "Method by which detector signal is acquired by the data system." [PSI:MS] relationship: part_of MS:1000453 ! detector [Term] id: MS:1000028 name: detector resolution def: "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." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000481 ! detector attribute [Term] id: MS:1000029 name: sampling frequency def: "The rate of signal sampling (measurement) with respect to time." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." synonym: "ADC Sampling Frequency" NARROW [] is_a: MS:1000481 ! detector attribute [Term] id: MS:1000030 name: vendor def: "Name of instrument vendor, replaced by MS:1000031 Model From Vendor." [PSI:MS] is_obsolete: true [Term] id: MS:1000031 name: instrument model def: "Instrument model name not including the vendor's name." [PSI:MS] relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000032 name: customization def: "Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000496 ! instrument attribute [Term] id: MS:1000033 name: deisotoping def: "The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000034 name: charge deconvolution def: "The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000035 name: peak picking def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000036 name: scan mode def: "TODO: Add definition." [PSI:MS] is_obsolete: true [Term] id: MS:1000037 name: polarity def: "Terms to describe the polarity setting of the instrument." [PSI:MS] relationship: part_of MS:1000459 ! spectrum instrument description [Term] id: MS:1000038 name: minute def: "Acquisition time in minutes. Replace by MS:1000016 - Scan Time." [PSI:MS] is_obsolete: true [Term] id: MS:1000039 name: second def: "Acquisition time in seconds. Replace by MS:1000016 - Scan Time." [PSI:MS] is_obsolete: true [Term] id: MS:1000040 name: m/z def: "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." [PSI:MS] synonym: "mass-to-charge ratio" EXACT [] synonym: "Th" EXACT [] synonym: "thomson" EXACT [] is_a: MS:1000460 ! unit [Term] id: MS:1000041 name: charge state def: "The charge state of the ion, single or multiple and positive or negatively charged." [PSI:MS] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute [Term] id: MS:1000042 name: intensity def: "Intensity of ions as measured by the height or area of a peak in a mass spectrum." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute [Term] id: MS:1000043 name: intensity unit def: "Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors." [PSI:MS] is_a: MS:1000460 ! unit [Term] id: MS:1000044 name: dissociation method def: "Fragmentation method used for dissociation or fragmentation." [PSI:MS] synonym: "Activation Method" RELATED [] relationship: part_of MS:1000456 ! precursor activation [Term] id: MS:1000045 name: collision energy def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000111 ! energy unit [Term] id: MS:1000046 name: energy unit def: "Energy units are represented in either eV or Joules. Obsoleted in favor of UO:0000111" [PSI:MS] is_a: MS:1000460 ! unit is_obsolete: true [Term] id: MS:1000047 name: emulsion def: "State if the sample is in emulsion form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000048 name: gas def: "State if the sample is in gaseous form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000049 name: liquid def: "State if the sample is in liquid form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000050 name: solid def: "State if the sample is in solid form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000051 name: solution def: "State if the sample is in solution form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000052 name: suspension def: "State if the sample is in suspension form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000053 name: sample batch def: "Sample batch lot identifier." [PSI:MS] is_a: MS:1000548 ! sample attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000054 name: chromatography def: "Chromatographic conditions used to obtain the sample." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000055 name: continuous flow fast atom bombardment def: "Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix." [PSI:MS] synonym: "CF-FAB" EXACT [] is_a: MS:1000007 ! inlet type [Term] id: MS:1000056 name: direct inlet def: "The sample is directly inserted into the ion source, usually on the end of a heatable probe." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000057 name: electrospray inlet def: "Inlet used for introducing the liquid sample into an electrospray ionization source." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000058 name: flow injection analysis def: "Sample is directly injected or infused into the ionization source." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000059 name: inductively coupled plasma def: "A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000060 name: infusion def: "The continuous flow of solution of a sample into the ionization source." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000061 name: jet separator def: "A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000062 name: membrane separator def: "A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000063 name: moving belt def: "Continuous moving surface in the form of a belt which passes through an ionsource carrying analyte molecules." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000064 name: moving wire def: "Continuous moving surface in the form of a wire which passes through an ionsource carrying analyte molecules." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000065 name: open split def: "A division of flowing stream of liquid into two streams." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000066 name: particle beam def: "Method for generating ions from a solution of an analyte." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000067 name: reservoir def: "A sample inlet method involving a reservoir." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000068 name: septum def: "A disc composed of a flexible material that seals the entrance to the reservoir. Can also be enterance to the vaccum chamber." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000069 name: thermospray inlet def: "A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000070 name: atmospheric pressure chemical ionization def: "Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization." [PSI:MS] synonym: "APCI" EXACT [] is_a: MS:1000240 ! atmospheric pressure ionization [Term] id: MS:1000071 name: chemical ionization def: "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." [PSI:MS] synonym: "CI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000072 name: Electronic Ionization def: "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. OBSOLETE because redundant replaced by MS:1000389 electron ionization" [PSI:MS] synonym: "EI" EXACT [] is_obsolete: true [Term] id: MS:1000073 name: electrospray ionization def: "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." [PSI:MS] synonym: "ESI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000074 name: fast atom bombardment ionization def: "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." [PSI:MS] synonym: "FAB" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000075 name: matrix-assisted laser desorption ionization def: "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." [PSI:MS] synonym: "MALDI" EXACT [] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000076 name: negative ion mode def: "TODO: Add defintion." [PSI:MS] is_obsolete: true [Term] id: MS:1000077 name: positive ion mode def: "TODO: Add definition." [PSI:MS] is_obsolete: true [Term] id: MS:1000078 name: axial ejection linear ion trap def: "A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer." [PSI:MS] is_a: MS:1000264 ! ion trap [Term] id: MS:1000079 name: fourier transform ion cyclotron resonance mass spectrometer def: "A mass spectrometer 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." [PSI:MS] synonym: "FT_ICR" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000080 name: magnetic sector def: "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." [PSI:MS] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000081 name: quadrupole def: "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." [PSI:MS] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000082 name: quadrupole ion trap def: "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." [PSI:MS] synonym: "Paul Ion trap" EXACT [] synonym: "QIT" EXACT [] synonym: "Quistor" EXACT [] is_a: MS:1000264 ! ion trap [Term] id: MS:1000083 name: radial ejection linear ion trap def: "A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer." [PSI:MS] is_a: MS:1000264 ! ion trap [Term] id: MS:1000084 name: time-of-flight def: "Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy." [PSI:MS] synonym: "TOF" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000085 name: baseline def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS] is_a: MS:1000012 ! resolution measurement method [Term] id: MS:1000086 name: full width at half-maximum def: "A measure of resolution represented as width of the peak at half peak height." [PSI:MS] synonym: "FWHM" EXACT [] is_a: MS:1000012 ! resolution measurement method [Term] id: MS:1000087 name: ten percent valley def: "An attribute of resolution when the ratio between adjacent signals is 10% of the signal height." [PSI:MS] is_a: MS:1000012 ! resolution measurement method [Term] id: MS:1000088 name: constant def: "When resolution is constant with respect to m/z." [PSI:MS] is_a: MS:1000013 ! resolution type [Term] id: MS:1000089 name: proportional def: "When resolution is proportional with respect to m/z." [PSI:MS] is_a: MS:1000013 ! resolution type [Term] id: MS:1000090 name: mass scan def: "A variation of instrument where a selected mass is scanned." [PSI:MS] is_a: MS:1000017 ! Scan Function [Term] id: MS:1000091 name: selected ion detection def: "Please see Single Ion Monitoring." [PSI:MS] is_a: MS:1000017 ! Scan Function [Term] id: MS:1000092 name: decreasing m/z scan def: "High to low direction in terms of m/z of the scan for scanning analyzers." [PSI:MS] is_a: MS:1000018 ! scan direction [Term] id: MS:1000093 name: increasing m/z scan def: "Low to high direction in terms of m/z of the scan for scanning analyzers." [PSI:MS] is_a: MS:1000018 ! scan direction [Term] id: MS:1000094 name: exponential def: "The mass scan is done in exponential mode." [PSI:MS] is_a: MS:1000019 ! scan law [Term] id: MS:1000095 name: linear def: "The mass scan is done in linear mode." [PSI:MS] is_a: MS:1000019 ! scan law [Term] id: MS:1000096 name: quadratic def: "The mass scan is done in quadratic mode." [PSI:MS] is_a: MS:1000019 ! scan law [Term] id: MS:1000097 name: constant neutral mass loss def: "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." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000098 name: multiple ion monitoring def: "Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000099 name: multiple reaction monitoring def: "This term is not recommended. See Selected Reaction Monitoring. Replace by MS:1000206 - Selected Reaction Monitoring." [PSI:MS] synonym: "MRM" EXACT [] is_obsolete: true [Term] id: MS:1000100 name: precursor ion scan def: "The specific scan function or process that will record a precursor ion spectrum." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000101 name: product ion scan def: "The specific scan function or process that records product ion spectrum." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000102 name: single ion monitoring def: "The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum. Remap to MS:1000205." [PSI:MS] is_obsolete: true [Term] id: MS:1000103 name: single reaction monitoring def: "See Selected Reaction Monitoring. remap to MS:1000102." [PSI:MS] is_obsolete: true [Term] id: MS:1000104 name: None ?? def: "None." [PSI:MS] is_obsolete: true [Term] id: MS:1000105 name: reflectron off def: "Reflectron is off." [PSI:MS] is_a: MS:1000021 ! reflectron state [Term] id: MS:1000106 name: reflectron on def: "Reflectron is on." [PSI:MS] is_a: MS:1000021 ! reflectron state [Term] id: MS:1000107 name: channeltron def: "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." [PSI:MS] synonym: "Channeltron Detector" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000108 name: conversion dynode electron multiplier def: "A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected." [PSI:MS] is_a: MS:1000346 ! conversion dynode [Term] id: MS:1000109 name: conversion dynode photomultiplier def: "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." [PSI:MS] synonym: "ion-to-photon detector" RELATED [] is_a: MS:1000346 ! conversion dynode [Term] id: MS:1000110 name: daly detector def: "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." [PSI:MS] synonym: "Daly" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000111 name: electron multiplier tube def: "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." [PSI:MS] synonym: "EMT" EXACT [] is_a: MS:1000253 ! electron multiplier [Term] id: MS:1000112 name: faraday cup def: "A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000113 name: focal plane array def: "An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS] is_a: MS:1000348 ! focal plane collector [Term] id: MS:1000114 name: microchannel plate detector def: "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." [PSI:MS] synonym: "multichannel plate" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000115 name: multi-collector def: "A detector system commonly used in inductively coupled plasma mass spectrometers." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000116 name: photomultiplier def: "A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected." [PSI:MS] synonym: "PMT" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000117 name: analog-digital converter def: "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." [PSI:MS] synonym: "ADC" EXACT [] is_a: MS:1000027 ! detector acquisition mode [Term] id: MS:1000118 name: pulse counting def: "Definition to do." [PSI:MS] is_a: MS:1000027 ! detector acquisition mode [Term] id: MS:1000119 name: time-digital converter def: "A device for converting a signal of sporadic pluses into a digital representation of their time indices." [PSI:MS] synonym: "TDC" EXACT [] is_a: MS:1000027 ! detector acquisition mode [Term] id: MS:1000120 name: transient recorder def: "A detector acquisition mode used for detecting transient signals." [PSI:MS] is_a: MS:1000027 ! detector acquisition mode [Term] id: MS:1000121 name: AB SCIEX instrument model def: "The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as \"Applied Biosystems|MDS SCIEX\"" [PSI:MS] synonym: "Applied Biosystems|MDS SCIEX" RELATED [] is_a: MS:1000031 ! instrument model [Term] id: MS:1000122 name: Bruker Daltonics instrument model def: "Bruker Daltonics instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000123 name: IonSpec instrument model def: "IonSpec corporation instrument model." [PSI:MS] is_a: MS:1000489 ! Varian instrument model [Term] id: MS:1000124 name: Shimadzu instrument model def: "Shimadzu corporation instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000125 name: Thermo Finnigan instrument model def: "ThermoFinnigan from Thermo Electron Corporation instrument model." [PSI:MS] is_a: MS:1000483 ! Thermo Fisher Scientific instrument model [Term] id: MS:1000126 name: Waters instrument model def: "Waters Corporation instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000127 name: centroid mass spectrum def: "Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset." [PSI:MS] synonym: "Discrete Mass Spectrum" EXACT [] is_a: MS:1000525 ! spectrum representation [Term] id: MS:1000128 name: profile mass spectrum def: "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." [PSI:MS] synonym: "continuous mass spectrum" EXACT [] synonym: "Continuum Mass Spectrum" EXACT [] is_a: MS:1000525 ! spectrum representation [Term] id: MS:1000129 name: negative scan def: "Polarity of the scan is negative." [PSI:MS] is_a: MS:1000037 ! polarity is_a: MS:1000465 ! scan polarity [Term] id: MS:1000130 name: positive scan def: "Polarity of the scan is positive." [PSI:MS] is_a: MS:1000037 ! polarity is_a: MS:1000465 ! scan polarity [Term] id: MS:1000131 name: number of counts def: "The number of counted events observed in one or a group of elements of a detector." [PSI:MS] is_a: MS:1000043 ! intensity unit [Term] id: MS:1000132 name: percent of base peak def: "The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000043 ! intensity unit [Term] id: MS:1000133 name: collision-induced dissociation def: "The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended." [PSI:MS] synonym: "CID" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000134 name: plasma desorption def: "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." [PSI:MS] synonym: "PD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000135 name: post-source decay def: "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." [PSI:MS] synonym: "PSD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000136 name: surface-induced dissociation def: "Fragmentation that results from the collision of an ion with a surface." [PSI:MS] synonym: "SID" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000137 name: electron volt def: "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." [PSI:MS] synonym: "eV" EXACT [] is_obsolete: true [Term] id: MS:1000138 name: percent collision energy def: "Collision energy required to fragment an ion represented as a percent value." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: UO:0000111 ! energy unit [Term] id: MS:1000139 name: 4000 Q TRAP def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000140 name: 4700 Proteomics Analyzer def: "Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS." [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000141 name: APEX IV def: "Bruker Daltonics APEX IV MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000142 name: APEX-Q def: "Bruker Daltonics APEX-Q MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000143 name: API 150EX def: "Applied Biosystems/MDS SCIEX API 150EX MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000144 name: API 150EX Prep def: "Applied Biosystems/MDS SCIEX API 150EX Prep MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000145 name: API 2000 def: "Applied Biosystems/MDS SCIEX API 2000 MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000146 name: API 3000 def: "Applied Biosystems/MDS SCIEX API 3000 MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000147 name: API 4000 def: "Applied Biosystems/MDS SCIEX API 4000 MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000148 name: autoFlex II def: "Bruker Daltonics autoFlex II MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000149 name: autoFlex TOF/TOF def: "Bruker Daltonics autoFlex TOF/TOF MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000150 name: Auto Spec Ultima NT def: "Waters AutoSpec Ultima NT MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000151 name: Bio TOF II def: "Bruker Daltonics BioTOF II MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000152 name: Bio TOF Q def: "Bruker Daltonics BioTOF Q MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000153 name: DELTA plusAdvantage def: "ThermoFinnigan DELTA plusAdvantage MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000154 name: DELTAplusXP def: "ThermoFinnigan DELTAplusXP MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000155 name: ELEMENT2 def: "ThermoFinnigan ELEMENT2 MS." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000156 name: esquire4000 def: "Bruker Daltonics esquire4000 MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000157 name: esquire6000 def: "Bruker Daltonics esquire6000 MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000158 name: explorer def: "IonSpec Explorer MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000159 name: GCT def: "Waters GCT MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000160 name: HCT def: "Bruker Daltonics HCT MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000161 name: HCT Plus def: "Bruker Daltonics HCTPlus MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000162 name: HiRes ESI def: "IonSpec HiResESI MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000163 name: HiRes MALDI def: "IonSpec HiResMALDI MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000164 name: IsoPrime def: "Waters IsoPrime MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000165 name: IsoProbe def: "Waters IsoProbe MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000166 name: IsoProbe T def: "Waters IsoProbe T MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000167 name: LCQ Advantage def: "ThermoFinnigan LCQ Advantage MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000168 name: LCQ Classic def: "ThermoFinnigan LCQ Classic MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000169 name: LCQ Deca XP Plus def: "ThermoFinnigan LCQ Deca XP Plus MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000170 name: M@LDI L def: "Waters MALDI L MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000171 name: M@LDI LR def: "Waters MALDI LR MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000172 name: MAT253 def: "ThermoFinnigan MAT253 MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000173 name: MAT900XP def: "ThermoFinnigan MAT900XP MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000174 name: MAT900XP Trap def: "ThermoFinnigan MAT900XP Trap MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000175 name: MAT95XP def: "ThermoFinnigan MAT95XP MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000176 name: MAT95XP Trap def: "ThermoFinnigan MAT95XP Trap MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000177 name: microFlex def: "Bruker Daltonics microFlex MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000178 name: microTOFLC def: "Bruker Daltonics microTOFLC MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000179 name: neptune def: "ThermoFinnigan NEPTUNE MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000180 name: NG-5400 def: "Waters NG-5400 MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000181 name: OMEGA def: "IonSpec OMEGA MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000182 name: OMEGA-2001 def: "IonSpec OMEGA-2001 MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000183 name: OmniFlex def: "Bruker Daltonics OminFlex MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000184 name: Platform ICP def: "Waters Platform ICP MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000185 name: PolarisQ def: "ThermoFinnigan PolarisQ MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000186 name: proteomics solution 1 def: "Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000187 name: Q TRAP def: "Applied Biosystems/MDS SCIEX Q TRAP MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000188 name: Q-Tof micro def: "Waters Q-Tof micro MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000189 name: Q-Tof ultima def: "Waters Q-Tof Ultima MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000190 name: QSTAR def: "Applied Biosystems/MDS SCIEX QSTAR MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000191 name: quattro micro def: "Waters Quattro micro MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000192 name: Quattro UItima def: "Waters Quattro Uitima MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000193 name: Surveyor MSQ def: "ThermoFinnigan Surveyor MSQ MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000194 name: SymBiot I def: "Applied Biosystems/MDS SCIEX SymBiot I MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000195 name: SymBiot XVI def: "Applied Biosystems/MDS SCIEX SymBiot XVI MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000196 name: TEMPUS TOF def: "ThermoFinnigan TEMPUS TOF MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000197 name: TRACE DSQ def: "ThermoFinnigan TRACE DSQ MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000198 name: TRITON def: "ThermoFinnigan TRITON MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000199 name: TSQ Quantum def: "ThermoFinnigan TSQ Quantum MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000200 name: ultima def: "IonSpec Ultima MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000201 name: ultraFlex def: "Bruker Daltonics ultraFlex MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000202 name: ultraFlex TOF/TOF def: "Bruker Daltonics ultraFlex TOF/TOF MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000203 name: Voyager-DE PRO def: "Applied Biosystems/MDS SCIEX Voyager-DE PRO MS." [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000204 name: Voyager-DE STR def: "Applied Biosystems/MDS SCIEX Voyager-DE STR MS." [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000205 name: selected ion monitoring def: "The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum." [PSI:MS] synonym: "MIM" RELATED [] synonym: "Multiple Ion Monitoring" EXACT [] synonym: "SIM" EXACT [] is_a: MS:1000479 ! purgatory [Term] id: MS:1000206 name: selected reaction monitoring def: "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." [PSI:MS] synonym: "MRM" RELATED [] synonym: "Multiple Reaction Monitoring" RELATED [] synonym: "SRM" EXACT [] is_a: MS:1000479 ! purgatory [Term] id: MS:1000207 name: accurate mass def: "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." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000507 ! ion attribute relationship: has_units UO:0000002 ! mass unit [Term] id: MS:1000208 name: average mass def: "The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000507 ! ion attribute relationship: has_units UO:0000002 ! mass unit [Term] id: MS:1000209 name: appearance energy def: "The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." synonym: "AE" EXACT [] is_a: MS:1000507 ! ion attribute relationship: has_units UO:0000111 ! energy unit [Term] id: MS:1000210 name: base peak def: "The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures." [PSI:MS] synonym: "BP" EXACT [] is_a: MS:1000231 ! peak [Term] id: MS:1000211 name: charge number def: "The total charge on an ion divided by the electron charge e." [PSI:MS] xref: value-type:xsd\:int "The allowed value-type for this CV term." synonym: "z" EXACT [] is_a: MS:1000507 ! ion attribute [Term] id: MS:1000212 name: dalton def: "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." [PSI:MS] synonym: "Da" EXACT [] is_obsolete: true [Term] id: MS:1000213 name: electron affinity def: "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." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." synonym: "EA" EXACT [] is_a: MS:1000507 ! ion attribute [Term] id: MS:1000214 name: electron energy obsolete def: "The potential difference through which electrons are accelerated before they are used to bring about electron ionization." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000215 name: exact mass def: "The calculated mass of an ion or molecule containing a single isotope of each atom." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000507 ! ion attribute relationship: has_units UO:0000002 ! mass unit [Term] id: MS:1000216 name: field-free region def: "A section of a mass spectrometer in which there are no electric or magnetic fields." [PSI:MS] synonym: "FFR" EXACT [] is_a: MS:1000487 ! ion optics attribute [Term] id: MS:1000217 name: ionization cross section def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000218 name: ioniazation efficiency def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used. See Ionization Efficiency." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_obsolete: true [Term] id: MS:1000219 name: ionization energy def: "The minimum energy required to remove an electron from an atom or molecule to produce a positive ion." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." synonym: "IE" EXACT [] is_a: MS:1000507 ! ion attribute relationship: has_units UO:0000111 ! energy unit [Term] id: MS:1000220 name: isotope dilution mass spectrometry def: "A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard." [PSI:MS] synonym: "IDMS" EXACT [] is_a: MS:1000268 ! mass spectrometry [Term] id: MS:1000221 name: magnetic deflection def: "The deflection of charged particles in a magnetic field due to a force equal to qv B 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." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000222 name: mass defect def: "The difference between the monoisotipic and nominal mass of a molecule or atom." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000507 ! ion attribute relationship: has_units UO:0000002 ! mass unit [Term] id: MS:1000223 name: mass number def: "The sum of the protons and neutrons in an atom, molecule or ion." [PSI:MS] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1000507 ! ion attribute [Term] id: MS:1000224 name: molecular mass def: "The mass of one mole of a molecular substance (6.022 1415(10) x 10^23 molecules)." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000507 ! ion attribute relationship: has_units UO:0000002 ! mass unit [Term] id: MS:1000225 name: monoisotopic mass def: "The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000507 ! ion attribute relationship: has_units UO:0000002 ! mass unit [Term] id: MS:1000226 name: molecular beam mass spectrometry def: "A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam." [PSI:MS] synonym: "MBMS" EXACT [] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000227 name: multiphoton ionization def: "Photoionization of an atom or molecule in which in two or more photons are absorbed." [PSI:MS] synonym: "MPI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000228 name: nitrogen rule def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000229 name: nominal mass def: "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." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000507 ! ion attribute relationship: has_units UO:0000002 ! mass unit [Term] id: MS:1000230 name: odd-electron rule def: "Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000231 name: peak def: "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." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000232 name: peak intensity def: "The height or area of a peak in a mass spectrum. Replaced by MS:1000505 Base Peak Intensity." [PSI:MS] is_obsolete: true [Term] id: MS:1000233 name: proton affinity def: "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." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." synonym: "PA" EXACT [PSI:MS] is_a: MS:1000507 ! ion attribute [Term] id: MS:1000234 name: mass resolving power def: "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." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000444 ! m/z Separation Method [Term] id: MS:1000235 name: total ion current chromatogram def: "Chromatogram obtained by plotting the total ion current detected in each of a series of mass spectra recorded as a function of retention time." [PSI:MS] synonym: "TIC chromatogram" EXACT [] is_a: MS:1000524 ! data file content is_a: MS:1000626 ! chromatogram type [Term] id: MS:1000236 name: transmission def: "The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000496 ! instrument attribute [Term] id: MS:1000237 name: unified atomic mass unit def: "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." [PSI:MS] synonym: "u" EXACT [] is_obsolete: true [Term] id: MS:1000238 name: accelerator mass spectrometry def: "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." [PSI:MS] synonym: "AMS" EXACT [] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000239 name: atmospheric pressure matrix-assisted laser desorption ionization def: "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." [PSI:MS] synonym: "AP MALDI" EXACT [] is_a: MS:1000240 ! atmospheric pressure ionization [Term] id: MS:1000240 name: atmospheric pressure ionization def: "Any ionization process in which ions are formed in the gas phase at atmospheric pressure." [PSI:MS] synonym: "API" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000241 name: Atmostpheric Pressure Photoionization def: "Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. OBSOLETE because redundant replace by MS:1000382 atmospheric pressure photoionization" [PSI:MS] synonym: "APPI" EXACT [] is_obsolete: true [Term] id: MS:1000242 name: blackbody infrared radiative dissociation def: "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." [PSI:MS] synonym: "BIRD" EXACT [] is_a: MS:1000044 ! dissociation method is_a: MS:1000437 ! ion reaction [Term] id: MS:1000243 name: charge-remote fragmentation def: "A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site." [PSI:MS] synonym: "CRF" EXACT [] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000244 name: consecutive reaction monitoring def: "MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] synonym: "CRM" EXACT [] is_a: MS:1000479 ! purgatory [Term] id: MS:1000245 name: charge stripping def: "The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion." [PSI:MS] synonym: "CS" EXACT [] is_a: MS:1000510 ! precursor activation attribute [Term] id: MS:1000246 name: delayed extraction def: "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." [PSI:MS] synonym: "DE" EXACT [] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000247 name: desorption ionization def: "The formation of ions from a solid or liquid material after the rapid vaporization of that sample." [PSI:MS] synonym: "DI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000248 name: direct insertion probe def: "A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization." [PSI:MS] synonym: "DIP" EXACT [] is_a: MS:1000007 ! inlet type [Term] id: MS:1000249 name: direct liquid introduction def: "The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization." [PSI:MS] synonym: "DLI" EXACT [] is_a: MS:1000007 ! inlet type [Term] id: MS:1000250 name: electron capture dissociation def: "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." [PSI:MS] synonym: "ECD" EXACT [] is_a: MS:1000044 ! dissociation method is_a: MS:1000437 ! ion reaction [Term] id: MS:1000251 name: even-electron ion def: "An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state." [PSI:MS] synonym: "EE" EXACT [] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000252 name: electron-induced excitation in organics def: "The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS] synonym: "EIEIO" EXACT [] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000253 name: electron multiplier def: "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." [PSI:MS] synonym: "EM" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000254 name: electrostatic energy analyzer def: "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." [PSI:MS] synonym: "ESA" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000255 name: flowing afterglow def: "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." [PSI:MS] synonym: "FA" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000256 name: high-field asymmetric waveform ion mobility spectrometry def: "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." [PSI:MS] synonym: "FAIMS" EXACT [] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000257 name: field desorption def: "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." [PSI:MS] synonym: "FD" EXACT [] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000258 name: field ionization def: "The removal of electrons from any species by interaction with a high electric field." [PSI:MS] synonym: "FI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000259 name: glow discharge ionization def: "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." [PSI:MS] synonym: "GD-MS" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000260 name: ion kinetic energy spectrometry def: "A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge." [PSI:MS] synonym: "IKES" EXACT [] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000261 name: ion mobility spectrometry def: "The separation of ions according to their velocity through a buffer gas under the influence of an electric field." [PSI:MS] synonym: "IMS" EXACT [] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000262 name: infrared multiphoton dissociation def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons." [PSI:MS] synonym: "IRMPD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000263 name: isotope ratio mass spectrometry def: "The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer." [PSI:MS] synonym: "IRMS" EXACT [] is_a: MS:1000268 ! mass spectrometry [Term] id: MS:1000264 name: ion trap def: "A device for spatially confining ions using electric and magnetic fields alone or in combination." [PSI:MS] synonym: "IT" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000265 name: kinetic energy release distribution def: "Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction." [PSI:MS] synonym: "KERD" EXACT [] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000266 name: Laser Desorption alt_id: MS:1000394 def: "The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules. OBSOLETE as redudant, replace by laser desorption ionization MS:1000393" [PSI:MS] synonym: "Laser Ionization MERGE" EXACT [] synonym: "LD" EXACT [] is_obsolete: true [Term] id: MS:1000267 name: mass analyzed ion kinetic energy spectrometry def: "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." [PSI:MS] synonym: "MIKES" EXACT [] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000268 name: mass spectrometry def: "The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments." [PSI:MS] synonym: "MS" EXACT [] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000269 name: mass spectrometry/mass spectrometry def: "The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions." [PSI:MS] synonym: "MS/MS" EXACT [] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000270 name: multiple stage mass spectrometry def: "Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions." [PSI:MS] synonym: "MSn" EXACT [] is_a: MS:1000445 ! sequential m/z separation method ? [Term] id: MS:1000271 name: Negative Ion chemical ionization def: "Chemical ionization that results in the formation of negative ions." [PSI:MS] synonym: "NICI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000272 name: neutralization reionization mass spectrometry def: "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." [PSI:MS] synonym: "NRMS" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000273 name: photoionization def: "The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended." [PSI:MS] synonym: "PI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000274 name: pyrolysis mass spectrometry def: "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." [PSI:MS] synonym: "PyMS" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000275 name: collision quadrupole def: "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." [PSI:MS] synonym: "q" EXACT [] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000276 name: resonance enhanced multiphoton ionization def: "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." [PSI:MS] synonym: "REMPI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000277 name: residual gas analyzer def: "A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber." [PSI:MS] synonym: "RGA" EXACT [] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000278 name: surface enhanced laser desorption ionization def: "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." [PSI:MS] synonym: "SELDI" EXACT [] is_a: MS:1000406 ! surface ionization [Term] id: MS:1000279 name: surface enhanced neat desorption def: "Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface." [PSI:MS] synonym: "SEND" EXACT [] is_a: MS:1000406 ! surface ionization [Term] id: MS:1000280 name: suface ionization def: "The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. OBSOLETE as redudant replace by MS:1000406 surface ionization" [PSI:MS] synonym: "SI" EXACT [] is_obsolete: true [Term] id: MS:1000281 name: selected ion flow tube def: "A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions." [PSI:MS] synonym: "SIFT" EXACT [] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000282 name: sustained off-resonance irradiation def: "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." [PSI:MS] synonym: "SORI" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000283 name: Spark Source Mass Spectrometry def: "Mass spectrometry using spark ionization. OBSOLETE because redundant, replace by spark ionization MS:1000404." [PSI:MS] synonym: "SSMS" EXACT [] is_obsolete: true [Term] id: MS:1000284 name: stored waveform inverse fourier transform def: "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 MS/MS experiments." [PSI:MS] synonym: "SWIFT" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000285 name: total ion current def: "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." [PSI:MS] synonym: "TIC" EXACT [] is_a: MS:1000499 ! spectrum attribute xref: value-type:xsd\:float "The allowed value-type for this CV term." [Term] id: MS:1000286 name: time lag focusing def: "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." [PSI:MS] synonym: "TLF" EXACT [] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000287 name: time-of-flight mass spectrometer def: "An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy." [PSI:MS] synonym: "TOF-MS" EXACT [] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000288 name: cyclotron def: "A device that uses an oscillating electric field and magnetic field to accelerate charged particles." [PSI:MS] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000289 name: double-focusing mass spectrometer def: "A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam." [PSI:MS] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000290 name: hybrid mass spectrometer def: "A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry." [PSI:MS] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000291 name: linear ion trap def: "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." [PSI:MS] is_a: MS:1000264 ! ion trap [Term] id: MS:1000292 name: mass spectrograph obsolete def: "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." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000293 name: mass spectrometer def: "An instrument that measures the mass-to-charge ratio and relative abundances of ions." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000294 name: mass spectrum def: "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)." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000295 name: mattauch-herzog geometry def: "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." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000296 name: nier-johnson geometry def: "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." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000297 name: paul ion trap def: "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." [PSI:MS] synonym: "quadrupole ion trap" RELATED [] is_a: MS:1000479 ! purgatory [Term] id: MS:1000298 name: prolate traochoidal mass spectrometer def: "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." [PSI:MS] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000299 name: quistor def: "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." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000300 name: reflectron def: "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." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000301 name: sector mass spectrometer def: "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." [PSI:MS] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000302 name: tandem mass spectrometer def: "A mass spectrometer designed for mass spectrometry/mass spectrometry." [PSI:MS] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000303 name: transmission quadrupole mass spectrometer def: "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." [PSI:MS] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000304 name: accelerating voltage def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000487 ! ion optics attribute relationship: has_units UO:0000217 ! electric potential difference [Term] id: MS:1000305 name: cyclotron motion def: "The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB." [PSI:MS] is_a: MS:1000444 ! m/z Separation Method [Term] id: MS:1000306 name: dynamic mass spectrometry def: "A mass spectrometer in which m/z separation using one or more electric fields that vary with time." [PSI:MS] is_a: MS:1000293 ! mass spectrometer [Term] id: MS:1000307 name: einzel lens def: "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." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000308 name: electric field strength def: "The magnitude of the force per unit charge at a given point in space." [PSI:MS] is_a: MS:1000487 ! ion optics attribute xref: value-type:xsd\:float "The allowed value-type for this CV term." [Term] id: MS:1000309 name: first stability region def: "The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000310 name: fringing field def: "The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000311 name: kinetic energy analyzer def: "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." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000312 name: mass limit def: "The m/z value above which ions cannot be detected in a mass spectrometer." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000313 name: scan m/z range? def: "The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000314 name: mass selective axial ejection def: "The use of mass selective instability to eject ions of selected m/z values from an ion trap." [PSI:MS] is_a: MS:1000444 ! m/z Separation Method [Term] id: MS:1000315 name: mass selective instability def: "A method for selective ejection of ions according to their m/z value in an ion trap." [PSI:MS] is_a: MS:1000444 ! m/z Separation Method [Term] id: MS:1000316 name: mathieu stability diagram def: "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." [PSI:MS] is_a: MS:1000444 ! m/z Separation Method [Term] id: MS:1000317 name: orthogonal extraction def: "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." [PSI:MS] is_a: MS:1000444 ! m/z Separation Method [Term] id: MS:1000318 name: resonance ion ejection def: "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." [PSI:MS] is_a: MS:1000444 ! m/z Separation Method [Term] id: MS:1000319 name: space charge effect def: "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." [PSI:MS] is_a: MS:1000487 ! ion optics attribute [Term] id: MS:1000320 name: static field def: "An electric or magnetic field that does not change in time." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000321 name: 2E Mass Spectrum def: "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." [PSI:MS] is_a: MS:1000445 ! sequential m/z separation method ? [Term] id: MS:1000322 name: charge inversion mass spectrum def: "The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z." [PSI:MS] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000323 name: constant neutral loss scan def: "Spectrum of all precursor ions that undergo a selected m/z decrement." [PSI:MS] synonym: "constant neutral mass loss scan" RELATED [] synonym: "fixed neutral fragment scan" RELATED [] is_a: MS:1000479 ! purgatory [Term] id: MS:1000324 name: constant neutral gain scan def: "Spectrum of all precursor ions that undergo a selected m/z increment." [PSI:MS] synonym: "Constant Neutral Mass Gain Scan" EXACT [] is_a: MS:1000479 ! purgatory [Term] id: MS:1000325 name: constant neutral gain spectrum def: "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." [PSI:MS] synonym: "constant neutral mass gain spectrum" EXACT [] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000326 name: constant neutral loss spectrum def: "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." [PSI:MS] synonym: "constant neutral mass loss spectrum" EXACT [] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000327 name: consecutive reaction monitoring def: "A type of MS/MS experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. OBSOLETE as redundant replace by consecutive reaction monitoring MS:1000244." [PSI:MS] is_obsolete: true [Term] id: MS:1000328 name: e/2 mass spectrum def: "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." [PSI:MS] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000329 name: linked scan def: "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." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000330 name: linked scan at constant b/e def: "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." [PSI:MS] is_a: MS:1000329 ! linked scan [Term] id: MS:1000331 name: Linked Scan at Constant E2/V def: "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 recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors." [PSI:MS] is_a: MS:1000329 ! linked scan [Term] id: MS:1000332 name: Linked Scan at Constant B2/E def: "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." [PSI:MS] is_a: MS:1000329 ! linked scan [Term] id: MS:1000333 name: Linked Scan at Constant B[1-(E/E0)]^1/2 / E def: "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." [PSI:MS] is_a: MS:1000329 ! linked scan [Term] id: MS:1000334 name: MS/MS in Time def: "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 discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time." [PSI:MS] is_a: MS:1000445 ! sequential m/z separation method ? [Term] id: MS:1000335 name: MS/MS in Space def: "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." [PSI:MS] is_a: MS:1000445 ! sequential m/z separation method ? [Term] id: MS:1000336 name: neutral loss def: "The loss of an uncharged species during a rearrangement process." [PSI:MS] is_a: MS:1000445 ! sequential m/z separation method ? [Term] id: MS:1000337 name: nth generation product ion def: "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." [PSI:MS] synonym: "granddaughter ion" RELATED [] is_a: MS:1000342 ! product ion [Term] id: MS:1000338 name: nth generation product ion scan def: "The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000339 name: nth generation product ion spectrum def: "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." [PSI:MS] is_a: MS:1000343 ! product ion spectrum [Term] id: MS:1000340 name: precursor ion def: "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 not recommended." [PSI:MS] synonym: "parent ion" RELATED [] is_a: MS:1000506 ! ion role [Term] id: MS:1000341 name: precursor ion spectrum def: "Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z" [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000342 name: product ion def: "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." [PSI:MS] synonym: "daughter ion" RELATED [] is_a: MS:1000506 ! ion role [Term] id: MS:1000343 name: product ion spectrum def: "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." [PSI:MS] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000344 name: progeny ion def: "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+." [PSI:MS] synonym: "Progeny Fragment Ion" EXACT [] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000345 name: array detector def: "Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000346 name: conversion dynode def: "A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000347 name: dynode def: "One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000348 name: focal plane collector def: "A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000349 name: ion-to-photon detector def: "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." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000350 name: point collector def: "A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000351 name: postacceleration detector def: "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." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000352 name: secondary electron def: "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?" [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000353 name: adduct ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000354 name: aromatic ion def: "A planar cyclic ion that obeys the Hckel (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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000355 name: analog ion def: "Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000356 name: anti-aromatic ion def: "A planar cyclic ion with 4n ? electrons and is therefore not aromatic." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000357 name: cationized molecule def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000358 name: cluster ion def: "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]-." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000359 name: Conventional ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000360 name: diagnostic ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000361 name: dimeric ion def: "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]+." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000362 name: distonic ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000363 name: enium ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000364 name: fragment ion def: "A product ion that results from the dissociation of a precursor ion. Replaced by MS:1000342- product ion." [PSI:MS] is_obsolete: true [Term] id: MS:1000365 name: ion def: "An atomic or molecular species having a net positive or negative electric charge." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000366 name: Isotopologue ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000367 name: Isotopomeric ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000368 name: metastable ion def: "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." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000369 name: molecular ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000370 name: negative ion def: "An atomic or molecular species having a net negative electric charge." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000371 name: non-classical ion def: "Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000372 name: onium ion def: "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+." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000373 name: principal ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000374 name: positive ion def: "An atomic or molecular species having a net positive electric charge." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000375 name: protonated molecule def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000376 name: radical ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000377 name: reference ion def: "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." [PSI:MS] is_a: MS:1000508 ! ion chemical type [Term] id: MS:1000378 name: stable ion def: "An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000379 name: unstable ion def: "An ion with sufficient enerrgy to dissociate within the ion source." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000380 name: adiabatic ionization def: "A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000381 name: associative ionization def: "An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000382 name: atmospheric pressure photoionization def: "Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS] is_a: MS:1000240 ! atmospheric pressure ionization [Term] id: MS:1000383 name: autodetachment def: "The formation of a neutral when a negative ion in a disrtete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000384 name: autoionization def: "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." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000385 name: charge exchange ionization def: "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." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000386 name: chemi-ionization def: "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." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000387 name: desorption/ionization on silicon def: "The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface." [PSI:MS] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000388 name: dissociative ionization def: "The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000389 name: electron ionization def: "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." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000390 name: ion desolvation def: "The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000391 name: ion-pair formation def: "The reaction of a molecule to form both a positive ion and negative ion fragment among the products." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000392 name: ionization efficiency def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute [Term] id: MS:1000393 name: laser desorption ionization def: "The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material." [PSI:MS] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000395 name: liquid secondary ionization def: "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." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000396 name: membrane inlet def: "A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000397 name: microelectrospray def: "Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanaoelectrospray." [PSI:MS] is_a: MS:1000073 ! electrospray ionization [Term] id: MS:1000398 name: nanoelectrospray def: "Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray." [PSI:MS] synonym: "nanospray" EXACT [] is_a: MS:1000073 ! electrospray ionization [Term] id: MS:1000399 name: penning ionization def: "Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000400 name: plasma desorption ionization def: "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." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000401 name: pre-ionization state def: "An electronic state capable of undergoing auto-Ionization." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000402 name: secondary ionization def: "The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000403 name: soft ionization def: "The formation of gas-phase ions without extensive fragmentation." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000404 name: spark ionization def: "The formation of ions from a solid material by an intermittent electrical discharge." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000405 name: surface-assisted laser desorption ionization def: "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." [PSI:MS] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000406 name: surface ionization def: "The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000407 name: thermal ionization def: "The ionization of a neutral species through contact with a high temperature surface." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000408 name: vertical ionization def: "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." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000409 name: association reaction def: "The reaction of an ion with a neutral species in which the reactants combine to form a single ion." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000410 name: alpha-cleavage def: "A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000411 name: beta-cleavage def: "A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000412 name: buffer gas def: "An inert gas used for collisional deactivation of internally excited ions." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute [Term] id: MS:1000413 name: charge-induced fragmentation def: "Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000414 name: charge inversion reaction def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000415 name: charge permutation reaction def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000416 name: charge stripping reaction def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000417 name: charge transfer reaction def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000418 name: collisional excitation def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000419 name: collision gas def: "An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute [Term] id: MS:1000420 name: heterolytic cleavage def: "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." [PSI:MS] synonym: "heterolysis" RELATED [] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000421 name: high energy collision def: "Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000422 name: high-energy collision-induced dissociation def: "A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000423 name: homolytic cleavage def: "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." [PSI:MS] synonym: "homolysis" RELATED [] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000424 name: hydrogen/deuterium exchange def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000425 name: ion energy loss spectrum def: "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." [PSI:MS] is_a: MS:1000479 ! purgatory [Term] id: MS:1000426 name: ionizing collision def: "The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000427 name: ion/molecule reaction def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000428 name: ion/neutral complex def: "A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000429 name: ion/neutral species reaction def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000430 name: ion/neutral species exchange reaction def: "In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000431 name: kinetic method def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000432 name: low energy collisions def: "A collision between an ion and neutral species with translational energy approximately 1000 eV or lower." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000433 name: low-energy collision-induced dissociation def: "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." [PSI:MS] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000434 name: McLafferty Rearrangement def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000435 name: photodissociation def: "A process wherein the reactant ion is dissociated as a result of absorption of one or more photons." [PSI:MS] synonym: "Multiphoton Dissociation" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000436 name: partial charge transfer reaction def: "Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000437 name: ion reaction def: "Chemical transformation involving an ion." [PSI:MS] relationship: part_of MS:1000365 ! ion [Term] id: MS:1000438 name: superelastic collision def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000439 name: surface-induced reaction def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000440 name: unimolecular dissociation def: "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." [PSI:MS] is_a: MS:1000437 ! ion reaction [Term] id: MS:1000441 name: scan def: "Function or process of the mass spectrometer where it records a spectrum." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000442 name: spectrum def: "A mass spectrum is an intensity vs m/z (mass-to-charge ratio) plot representing a chemical analysis." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000443 name: mass analyzer type def: "Mass analyzer separates the ions according to their mass-to-charge ratio." [PSI:MS] relationship: part_of MS:1000451 ! mass analyzer [Term] id: MS:1000444 name: m/z Separation Method def: "TODO: Add definition." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000445 name: sequential m/z separation method ? def: "TODO: Add definition." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000446 name: fast ion bombardment def: "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." [PSI:MS] synonym: "FIB" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000447 name: LTQ def: "Finnigan LTQ MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000448 name: LTQ FT def: "Finnigan LTQ FT MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000449 name: LTQ Orbitrap def: "Finnigan LTQ Orbitrap MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000450 name: LXQ def: "Finnigan LXQ MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000451 name: mass analyzer def: "Terms used to describe the Analyzer." [PSI:MS] relationship: part_of MS:1000463 ! instrument synonym: "analyzer" EXACT [] [Term] id: MS:1000452 name: data transformation def: "Terms used to describe types of data processing." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology synonym: "data processing" EXACT [] [Term] id: MS:1000453 name: detector def: "The device that detects ions." [PSI:MS] relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000454 name: instrument additional description def: "Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000455 name: ion selection attribute def: "Ion selection properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000456 name: precursor activation def: "Terms to describe the precursor activation." [PSI:MS] relationship: part_of MS:1000442 ! spectrum synonym: "activation" EXACT [] [Term] id: MS:1000457 name: sample def: "Terms to describe the sample." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000458 name: source def: "Terms to describe the source." [PSI:MS] relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000459 name: spectrum instrument description def: "Terms used to describe the spectrum." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000460 name: unit def: "Terms to describe units." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000461 name: additional description def: "Terms to describe Additional." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000462 name: ion optics def: "Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions." [PSI:MS] relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000463 name: instrument def: "Description of the instrument or the mass spectrometer." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology synonym: "instrument configuration" EXACT [] [Term] id: MS:1000464 name: mass unit def: "A unit of measurement for mass." [PSI:MS] is_obsolete: true [Term] id: MS:1000465 name: scan polarity def: "An acquisition mode to which specifies weather polarity is negative, positive or alternating." [PSI:MS] relationship: part_of MS:1000441 ! scan [Term] id: MS:1000466 name: alternating def: "Alternating." [PSI:MS] is_obsolete: true [Term] id: MS:1000467 name: 1200 series LC/MSD SL def: "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 MS/MS and 11 stages of manual MS/MS." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000468 name: 6110 Quadrupole LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000469 name: 6120 Quadrupole LC/MS def: "The 6120 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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000470 name: 6130 Quadrupole LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000471 name: 6140 Quadrupole LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000472 name: 6210 Time-of-Flight LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000473 name: 6310 Ion Trap LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000474 name: 6320 Ion Trap LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000475 name: 6330 Ion Trap LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000476 name: 6340 Ion Trap LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000477 name: 6410 Triple Quadrupole LC/MS def: "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." [PSI:MS] synonym: "6410 Triple Quad LC/MS" EXACT [] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000478 name: 1200 series LC/MSD VL def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000479 name: purgatory def: "Terms that will likely become obsolete unless there are wails of dissent." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000480 name: mass analyzer attribute def: "Analyzer properties that are associated with a value." [PSI:MS] relationship: part_of MS:1000451 ! mass analyzer [Term] id: MS:1000481 name: detector attribute def: "Detector attribute recognized as a value." [PSI:MS] relationship: part_of MS:1000453 ! detector [Term] id: MS:1000482 name: source attribute def: "Property of a source device that need a value." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1000483 name: Thermo Fisher Scientific instrument model def: "Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific." [PSI:MS] synonym: "Thermo Scientific" RELATED [] is_a: MS:1000031 ! instrument model [Term] id: MS:1000484 name: orbitrap def: "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." [PSI:MS] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000485 name: nanospray inlet def: "Nanospray Inlet." [PSI:MS] is_a: MS:1000057 ! electrospray inlet [Term] id: MS:1000486 name: source potential def: "Potential difference at the MS source in volts." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute relationship: has_units UO:0000217 ! electric potential difference [Term] id: MS:1000487 name: ion optics attribute def: "Ion optics involves components that help focus ion streams in mass spectrometry." [PSI:MS] is_a: MS:1000462 ! ion optics [Term] id: MS:1000488 name: Hitachi instrument model def: "Hitachi instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000489 name: Varian instrument model def: "Varian instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000490 name: Agilent instrument model def: "Agilent instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000491 name: Dionex instrument model def: "Dionex instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000492 name: Thermo Electron instrument model def: "Thermo Electron Corporation instrument model." [PSI:MS] is_a: MS:1000483 ! Thermo Fisher Scientific instrument model [Term] id: MS:1000493 name: Finnigan MAT instrument model def: "Finnigan MAT instrument model." [PSI:MS] is_a: MS:1000483 ! Thermo Fisher Scientific instrument model [Term] id: MS:1000494 name: Thermo Scientific instrument model def: "Thermo Scientific instrument model." [PSI:MS] is_a: MS:1000483 ! Thermo Fisher Scientific instrument model [Term] id: MS:1000495 name: Applied Biosystems instrument model def: "Applied Biosystems instrument model." [PSI:MS] synonym: "ABI" EXACT [] is_a: MS:1000031 ! instrument model [Term] id: MS:1000496 name: instrument attribute def: "Instrument properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000497 name: zoom scan def: "Special scan mode, where data with improved resoltuion is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS] is_a: MS:1000499 ! spectrum attribute synonym: "enhanced resolution scan" EXACT [] [Term] id: MS:1000498 name: full scan def: "Feature of the ion trap mass spectrometer where MS data is acquired over a mass range." [PSI:MS] is_a: MS:1000020 ! scanning method [Term] id: MS:1000499 name: spectrum attribute def: "Spectrum properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000500 name: scan m/z upper limit def: "The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." synonym: "mzRangeStop" RELATED [] is_a: MS:1000549 ! selection window attribute relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000501 name: scan m/z lower limit def: "The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." synonym: "mzRangeStart" RELATED [] is_a: MS:1000549 ! selection window attribute relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000502 name: dwell time def: "The time spent gathering data across a peak." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." synonym: "Scan Duration" RELATED [] is_a: MS:1000549 ! selection window attribute relationship: has_units UO:0000003 ! time unit [Term] id: MS:1000503 name: scan attribute def: "Scan properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000441 ! scan [Term] id: MS:1000504 name: base peak m/z def: "M/z value of the greatest peak in the mass spectrum." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000499 ! spectrum attribute relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000505 name: base peak intensity def: "The intensity of the greatest peak in the mass spectrum." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1000506 name: ion role def: "Ion Role." [PSI:MS] relationship: part_of MS:1000365 ! ion [Term] id: MS:1000507 name: ion attribute def: "Ion properties that are associated with a value." [PSI:MS] relationship: part_of MS:1000365 ! ion [Term] id: MS:1000508 name: ion chemical type def: "Ion Type." [PSI:MS] relationship: part_of MS:1000365 ! ion [Term] id: MS:1000509 name: activation energy def: "Activation Energy." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000111 ! energy unit [Term] id: MS:1000510 name: precursor activation attribute def: "Precursor Activation Attribute." [PSI:MS] relationship: part_of MS:1000456 ! precursor activation [Term] id: MS:1000511 name: ms level def: "Stages of ms achieved in a multi stage mass spectrometry experiment." [PSI:MS] xref: value-type:xsd\:int" The allowed value-type for this CV term." is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1000512 name: filter string def: "A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute [Term] id: MS:1000513 name: binary data array def: "A data array of values." [PSI:MS] relationship: part_of MS:1000442 ! spectrum relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000514 name: m/z array def: "A data array of mass divided by charge values." [PSI:MS] is_a: MS:1000513 ! binary data array relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000515 name: intensity array def: "A data array of intensity values." [PSI:MS] is_a: MS:1000513 ! binary data array [Term] id: MS:1000516 name: charge array def: "A data array of charge values." [PSI:MS] is_a: MS:1000513 ! binary data array [Term] id: MS:1000517 name: signal to noise array def: "A data array of signal-to-noise values." [PSI:MS] is_a: MS:1000513 ! binary data array [Term] id: MS:1000518 name: binary data type def: "Binary Data type. 16-bit integer, 32-bit integer, 32-bit float 64-bit integer 64-bit float." [PSI:MS] relationship: part_of MS:1000442 ! spectrum relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000519 name: 32-bit integer def: "Signed 32-bit integer." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1000520 name: 16-bit float def: "Signed 16-bit float." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1000521 name: 32-bit float def: "Signed 32-bit float. IEEE-754." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1000522 name: 64-bit integer def: "Signed 64-bit integer." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1000523 name: 64-bit float def: "Signed 64-bit float. IEEE-754." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1000524 name: data file content def: "Describes the data content on the file." [PSI:MS] relationship: part_of MS:1000577 ! data file [Term] id: MS:1000525 name: spectrum representation def: "Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks." [PSI:MS] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000526 name: MassLynx raw format def: "MassLynx raw file format, which is actually a directory/folder containing several files for each ms run." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000527 name: highest m/z value def: "Highest m/z value observed in the mass spectum." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000499 ! spectrum attribute relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000528 name: lowest m/z value def: "Lowest m/z value observed in the mass spectrum." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000499 ! spectrum attribute relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000529 name: instrument serial number def: "Serial Number of the instrument." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000496 ! instrument attribute [Term] id: MS:1000530 name: file format conversion def: "Conversion of one file format to another." [PSI:MS] is_a: MS:1000452 ! data transformation [Term] id: MS:1000531 name: software def: "Software related to the recording or transformation of spectra." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000532 name: Xcalibur def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS] is_a: MS:1000693 ! Thermo Finnigan software [Term] id: MS:1000533 name: Bioworks def: "Thermo Finnigan software for data analysis of peptides and proteins." [PSI:MS] synonym: "Bioworks Browser" RELATED [] is_a: MS:1000693 ! Thermo Finnigan software [Term] id: MS:1000534 name: Masslynx def: "Miromass software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000535 name: FlexAnalysis def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000536 name: data explorer def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000691 ! Applied Biosystems software [Term] id: MS:1000537 name: 4700 Explorer def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000691 ! Applied Biosystems software [Term] id: MS:1000538 name: massWolf def: "A software for converting Waters raw directory format to mzXML or mzML. massWolf was originally developed at the Institute for Systems Biology." [PSI:MS] is_a: MS:1000531 ! software synonym: "wolf" EXACT [] [Term] id: MS:1000539 name: Voyager Biospectrometry Workstation System def: "Applied Biosystems MALDI-TOF data acquisition and analysis system." [PSI:MS] is_a: MS:1000691 ! Applied Biosystems software [Term] id: MS:1000540 name: FlexControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000541 name: ReAdW def: "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\"." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000542 name: MzStar def: "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." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000543 name: data processing action def: "Data processing attribute used to describe the type of data processing performed on the data file." [PSI:MS] is_a: MS:1000452 ! data transformation [Term] id: MS:1000544 name: Conversion to mzML def: "Conversion of a file format to Proteomics Standards Initiative mzData file format." [PSI:MS] is_a: MS:1000530 ! file format conversion [Term] id: MS:1000545 name: Conversion to mzXML def: "Conversion of a file format to Institute of Systems Biology mzXML file format." [PSI:MS] is_a: MS:1000530 ! file format conversion [Term] id: MS:1000546 name: Conversion to mzData def: "Conversion of a file format to Proteomics Standards Initiative mzData file format." [PSI:MS] is_a: MS:1000530 ! file format conversion [Term] id: MS:1000547 name: object attribute def: "Object Attribute." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000548 name: sample attribute def: "Sample properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000457 ! sample [Term] id: MS:1000549 name: selection window attribute def: "Selection window properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000441 ! scan [Term] id: MS:1000550 name: time unit def: "Time Unit." [PSI:MS] is_obsolete: true [Term] id: MS:1000551 name: Analyst def: "AB SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000552 name: maldi spot identifier def: "Maldi Spot Identifier." [PSI:MS] relationship: part_of MS:1000479 ! purgatory [Term] id: MS:1000553 name: Trapper def: "A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000554 name: LCQ Deca def: "ThermoFinnigan LCQ Deca." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000555 name: LTQ Orbitrap Discovery def: "LTQ Orbitrap Discovery." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000556 name: LTQ Orbitrap XL def: "LTQ Orbitrap XL." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000557 name: LTQ FT Ultra def: "LTQ FT Ultra." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000558 name: GC Quantum def: "GC Quantum." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000559 name: spectrum type def: "Spectrum type." [PSI:MS] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000560 name: source file type def: "The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format." [PSI:MS] relationship: part_of MS:1000577 ! data file [Term] id: MS:1000561 name: data file checksum type def: "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data." [PSI:MS] relationship: part_of MS:1000577 ! data file [Term] id: MS:1000562 name: wiff file def: "Applied Biosystems wiff file format." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000563 name: Xcalibur RAW file def: "Thermo Finnigan RAW file format." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000564 name: mzData file def: "Proteomics Standards Inititative mzData file format." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000565 name: pkl file def: "Micromass pkl file format." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000566 name: mzXML file def: "Institute of Systems Biology mzXML file format." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000567 name: yep file def: "Bruker yep file format." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000568 name: MD5 def: "MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS] is_a: MS:1000561 ! data file checksum type xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000569 name: SHA-1 def: "SHA-1 (Secure Hash Algorithm-1) 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." [PSI:MS] is_a: MS:1000561 ! data file checksum type xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000570 name: spectra combination def: "Method used to combine the mass spectra." [PSI:MS] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000571 name: sum of spectra def: "Spectra Sum." [PSI:MS] is_a: MS:1000570 ! spectra combination [Term] id: MS:1000572 name: binary data compression type def: "Compression Type." [PSI:MS] relationship: part_of MS:1000442 ! spectrum relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000573 name: median of spectra def: "Spectra is combined by calculating the median of the spectra." [PSI:MS] is_a: MS:1000570 ! spectra combination [Term] id: MS:1000574 name: zlib compression def: "Zlib." [PSI:MS] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1000575 name: mean of spectra def: "Spectra is combined by calculating the mean of the spectra." [PSI:MS] is_a: MS:1000570 ! spectra combination [Term] id: MS:1000576 name: no compression def: "No Compression." [PSI:MS] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1000577 name: data file def: "Describes the type of file and its content." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology synonym: "source file" EXACT [] [Term] id: MS:1000578 name: LCQ Fleet def: "LCQ Fleet." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000579 name: MS1 spectrum def: "MS1 refers to single-stage MS/MS experiments designed to record the first stage of the product ion spectra." [PSI:MS] synonym: "Single-Stage Mass Spectrometry" EXACT [] synonym: "Q1 spectrum" EXACT [] synonym: "Q3 spectrum" EXACT [] synonym: "full spectrum" EXACT [] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000580 name: MSn spectrum def: "MSn refers to multi-stage MS/MS 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." [PSI:MS] synonym: "multiple-stage mass spectrometry spectrum" EXACT [] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type synonym: "product ion spectrum" EXACT [] [Term] id: MS:1000581 name: CRM spectrum def: "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." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000582 name: SIM spectrum def: "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)." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type synonym: "MIM spectrum" EXACT [] synonym: "multiple ion monitoring spectrum" EXACT [] synonym: "selected ion monitoring spectrum" EXACT [] [Term] id: MS:1000583 name: SRM spectrum def: "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." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type synonym: "MRM spectrum" EXACT [] synonym: "multiple reaction monitoring spectrum" EXACT [] synonym: "selected reaction monitoring spectrum" EXACT [] [Term] id: MS:1000584 name: mzML file def: "Proteomics Standards Inititative mzML file format." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000585 name: contact person attribute def: "Details about a person to contact in case of concern or dicussion about the file." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000577 ! data file [Term] id: MS:1000586 name: contact name def: "Name of a contact person." [PSI:MS] is_a: MS:1000585 ! contact person attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000587 name: contact address def: "Postal address of a contact person." [PSI:MS] is_a: MS:1000585 ! contact person attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000588 name: contact URL def: "Uniform Resource Locator related to the contact person." [PSI:MS] is_a: MS:1000585 ! contact person attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000589 name: contact email def: "Email adress of the contact person." [PSI:MS] is_a: MS:1000585 ! contact person attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000590 name: contact organization def: "Home institution of the contact person." [PSI:MS] is_a: MS:1000585 ! contact person attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000591 name: MzWiff def: "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." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000592 name: smoothing def: "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." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000593 name: baseline reduction def: "A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000594 name: low intensity data point removal def: "The removal of very low intensity data points that are likely to be spurious noise rather than real signal." [PSI:MS] synonym: "thresholding" EXACT [] is_a: MS:1000543 ! data processing action [Term] id: MS:1000595 name: time array def: "A data array of relative time offset values from a reference time." [PSI:MS] is_a: MS:1000513 ! binary data array relationship: has_units UO:0000003 ! time unit [Term] id: MS:1000596 name: measurement method def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000597 name: ion optics type def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] is_a: MS:1000462 ! ion optics [Term] id: MS:1000598 name: electron transfer dissociation def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them." [PSI:MS] synonym: "ETD" EXACT [] is_a: MS:1000044 ! dissociation method is_a: MS:1000437 ! ion reaction [Term] id: MS:1000599 name: pulsed q dissociation def: "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." [PSI:MS] synonym: "PQD" EXACT [] is_a: MS:1000044 ! dissociation method is_a: MS:1000437 ! ion reaction [Term] id: MS:1000600 name: Proteios def: "Database application and analysis platform for proteomics." [PSI:MS, source:www.proteios.org] is_a: MS:1000531 ! software [Term] id: MS:1000601 name: ProteinLynx Global Server def: "Waters software for data analysis." [PSI:MS] is_a: MS:1000694 ! Waters software [Term] id: MS:1000602 name: Shimadzu Biotech instrument model def: "Shimadzu Biotech instrument model." [PSI:MS] is_a: MS:1000124 ! Shimadzu instrument model [Term] id: MS:1000603 name: Shimadzu Scientific Instruments instrument model def: "Shimadzu Scientific Instruments instrument model." [PSI:MS] is_a: MS:1000124 ! Shimadzu instrument model [Term] id: MS:1000604 name: LCMS-IT-TOF def: "Shimadzu Scientific Instruments LCMS-IT-TOF MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1000605 name: LCMS-2010EV def: "Shimadzu Scientific Instruments LCMS-2010EV MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1000606 name: LCMS-2010A def: "Shimadzu Scientific Instruments LCMS-2010A MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1000607 name: AXIMA CFR MALDI-TOF def: "Shimadzu Biotech AXIMA CFR MALDI-TOF MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu Biotech instrument model [Term] id: MS:1000608 name: AXIMA-QIT def: "Shimadzu Biotech AXIMA-QIT MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu Biotech instrument model [Term] id: MS:1000609 name: AXIMA-CFR plus def: "Shimadzu Biotech AXIMA-CFR plus MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu Biotech instrument model [Term] id: MS:1000610 name: AXIMA Performance MALDI-TOF/TOF def: "Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu Biotech instrument model [Term] id: MS:1000611 name: AXIMA Confidence MALDI-TOF def: "Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu Biotech instrument model [Term] id: MS:1000612 name: AXIMA Assurance Linear MALDI-TOF def: "Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu Biotech instrument model [Term] id: MS:1000613 name: dta file def: "Peak list file format that should be better defined FIXME." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000614 name: ProteinLynx Global Server mass spectrum XML file def: "Peak list file format used by ProteinLynx Global Server." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000615 name: ProteoWizard def: "ProteoWizard software for data analysis. Currently developed and maintained by Darren Kessner at Parag Mallick's lab SFCAP at Cedars-Sinai." [PSI:MS] synonym: "pwiz" EXACT [] is_a: MS:1000531 ! software [Term] id: MS:1000616 name: preset scan configuration def: "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." [PSI:MS] is_a: MS:1000503 ! scan attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000617 name: wavelength array def: "A data array of electromagnetic radiation wavelength values." [PSI:MS] is_a: MS:1000513 ! binary data array [Term] id: MS:1000618 name: highest wavelength value def: "Highest wavelength value observed in the uv/vis spectum." [PSI:MS] is_a: MS:1000499 ! spectrum attribute xref: value-type:xsd\:float "The allowed value-type for this CV term." [Term] id: MS:1000619 name: lowest wavelength value def: "Lowest wavelength value observed in the uv/vis spectrum." [PSI:MS] is_a: MS:1000499 ! spectrum attribute xref: value-type:xsd\:float "The allowed value-type for this CV term." [Term] id: MS:1000620 name: PDA spectrum def: "Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum)." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000621 name: photodiode array detector def: "An array detector used to record spectra in the ultraviolet and visable region of light." [PSI:MS] synonym: "PDA" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000622 name: Surveyor PDA def: "Surveyor PDA." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000623 name: Accela PDA def: "Accela PDA." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000624 name: inductive detector def: "Inductive detector." [PSI:MS] synonym: "image current detector" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000625 name: chromatogram def: "The representation of detector response versus time." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1000626 name: chromatogram type def: "Broad category or type of a chromatogram." [PSI:MS] relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000627 name: selected ion current chromatogram def: "Chromatogram created by creating an array of the measurements of a specific single ion current at each time point." [PSI:MS] synonym: "SIC chromatogram" EXACT [] is_a: MS:1000524 ! data file content is_a: MS:1000626 ! chromatogram type [Term] id: MS:1000628 name: basepeak chromatogram def: "Chromatogram created by creating an array of the most intense peaks at each time point." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000626 ! chromatogram type [Term] id: MS:1000629 name: low intensity threshold def: "Threshold below which some action is taken." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:1000630 name: data processing parameter def: "Data processing parameter used in the data processing performed on the data file." [PSI:MS] is_a: MS:1000452 ! data transformation [Term] id: MS:1000631 name: high intensity threshold def: "Threshold above which some action is taken." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:1000632 name: Q-Tof Premier def: "Waters Q-Tof Premier MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000633 name: possible charge state def: "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." [PSI:MS] xref: value-type:xsd\:int" The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute [Term] id: MS:1000634 name: DSQ def: "ThermoFinnigan DSQ GC-MS" [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000635 name: ITQ 700 def: "Thermo Scientific ITQ 700 GC-MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000636 name: ITQ 900 def: "Thermo Scientific ITQ 900 GC-MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000637 name: ITQ 1100 def: "Thermo Scientific ITQ 1100 GC-MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000638 name: LTQ XL ETD def: "Thermo Scientific LTQ XL MS with ETD" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000639 name: LTQ Orbitrap XL ETD def: "Thermo Scientific LTQ Orbitrap XL MS with ETD" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000640 name: DFS def: "Thermo Scientific DFS HR GC-MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000641 name: DSQ II def: "Thermo Scientific DSQ II GC-MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000642 name: MALDI LTQ XL def: "Thermo Scientific MALDI LTQ XL MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000643 name: MALDI LTQ Orbitrap def: "Thermo Scientific MALDI LTQ Orbitrap MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000644 name: TSQ Quantum Access def: "Thermo Scientific TSQ Quantum Access MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000645 name: Element XR def: "Thermo Scientific Element XR HR-ICP-MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000646 name: Element 2 def: "Thermo Scientific Element 2 HR-ICP-MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000647 name: Element GD def: "Thermo Scientific Element GD Glow Discharge MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000648 name: GC IsoLink def: "Thermo Scientific GC IsoLink Isotope Ratio MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000649 name: Exactive def: "Thermo Scientific Exactive MS" [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000650 name: Proteomics Discoverer def: "Thermo Scientific software for data analysis of peptides and proteins." [PSI:MS] is_a: MS:1000693 ! Thermo Finnigan software [Term] id: MS:1000651 name: 3200 QTRAP def: "AB SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200" [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000652 name: 4800 Plus MALDI TOF-TOF Analyzer def: "AB SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer" [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000653 name: API 3200 def: "AB SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000654 name: API 5000 def: "AB SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000655 name: QSTAR Elite def: "AB SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite" [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000656 name: QSTAR Pulsar def: "Applied Biosystems|MDS SCIEX QSTAR Pulsar" [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000657 name: QSTAR XL def: "Applied Biosystems|MDS SCIEX QSTAR XL" [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000658 name: 4800 Proteomics Analyzer def: "Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer" [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000659 name: 4000 Series Explorer Software def: "AB SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000661 name: GPS Explorer def: "AB SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000662 name: LightSight Software def: "AB SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000663 name: ProteinPilot Software def: "AB SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000664 name: TissueView Software def: "Applied Biosystems|MDS SCIEX software for tissue imaging." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000665 name: MarkerView Software def: "Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000666 name: MRMPilot Software def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000667 name: BioAnalyst def: "Applied Biosystems|MDS SCIEX software for bio-related data exploration." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000668 name: Pro ID def: "Applied Biosystems|MDS SCIEX software for protein identification." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000669 name: Pro ICAT def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000670 name: Pro Quant def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000671 name: Pro BLAST def: "Applied Biosystems|MDS SCIEX software for MS-BLAST identification." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000672 name: Cliquid? def: "AB SCIEX or Applied Biosystems software." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000673 name: MIDAS Workflow Designer def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000674 name: MultiQuant def: "Applied Biosystems|MDS SCIEX software for MRM-based quantitation." [PSI:MS] is_a: MS:1000690 ! AB SCIEX software [Term] id: MS:1000675 name: 6220 Time-of-Flight LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000676 name: 6510 Quadrupole Time-of-Flight LC/MS def: "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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000677 name: 6520 Quadrupole Time-of-Flight LC/MS def: "The 6520 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." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000678 name: MassHunter Data Acquisition def: "Software for data acquisition of 6000 series instruments." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000679 name: MassHunter Easy Access def: "Software for open access data acquisition." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000680 name: MassHunter Qualitative Analysis def: "Software for data analysis of data from 6000 series instruments." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000681 name: MassHunter Quantitative Analysis def: "Software for quantitation of Triple Quadruople and Quadrupole Time-of-Flight data." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000682 name: MassHunter Metabolite ID def: "Software for identification of metabolites." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000683 name: MassHunter BioConfirm def: "Software for protein characterization." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000684 name: Genespring MS def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000685 name: MassHunter Mass Profiler def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000686 name: METLIN def: "Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000687 name: Spectrum Mill for MassHunter Workstation def: "Software for protein identification and characterization of complex protein digest mixtures." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000688 name: 6300 Series Ion Trap Data Analysis Software def: "Software for data analysis of 6300 series ion trap mass spectrometers." [PSI:MS] is_a: MS:1000689 ! Agilent software [Term] id: MS:1000689 name: Agilent software def: "Agilent software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000690 name: AB SCIEX software def: "AB SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000691 name: Applied Biosystems software def: "Applied Biosystems|MDS SCIEX software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000692 name: Bruker software def: "Bruker software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000693 name: Thermo Finnigan software def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS] synonym: "Bioworks Browser" RELATED [] is_a: MS:1000531 ! software [Term] id: MS:1000694 name: Waters software def: "Waters software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000695 name: apex ultra def: "Bruker Daltonics apex ultra" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000696 name: autoflex III smartbeam def: "Bruker Daltonics autoflex III smartbeam" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000697 name: HCT Series def: "Bruker Daltonics HCT Series" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000698 name: HCTultra def: "Bruker Daltonics HCTultra" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000699 name: HCTultra PTM def: "Bruker Daltonics HCTultra PTM Discovery System" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000700 name: HCTultra ETD II def: "Bruker Daltonics HCTultra ETD II System" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000701 name: microflex LT def: "Bruker Daltonics microflex MS." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000702 name: micrOTOF def: "Bruker Daltonics micrOTOF" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000703 name: micrOTOF-Q def: "Bruker Daltonics micrOTOF-Q" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000704 name: micrOTOF-Q II def: "Bruker Daltonics micrOTOF-Q II" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000705 name: ultraflex III TOF/TOF def: "Bruker Daltonics ultraflex III TOF/TOF" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000706 name: apexControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000707 name: BioTools def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000708 name: CLINPROT def: "Bruker CLINPROT software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000709 name: CLINPROT micro def: "Bruker CLINPROT micro software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000710 name: CLINPROT robot def: "Bruker CLINPROT robot software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000711 name: ClinProTools def: "Bruker ClinProTools software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000712 name: Compass def: "Bruker Compass software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000713 name: Compass for HCT/esquire def: "Bruker Compass for HCT/esquire software" [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000714 name: Compass for micrOTOF def: "Bruker Compass for micrOTOF software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000715 name: Compass OpenAccess def: "Bruker compass OpenAccess software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000716 name: Compass Security Pack def: "Bruker compass Security Pack software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000717 name: CompassXport def: "Bruker stand-alone software for data conversion." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000718 name: CompassXtract def: "Bruker software library for data access." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000719 name: DataAnalysis def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000720 name: dpControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000721 name: esquireControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000722 name: flexImaging def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000723 name: GENOLINK def: "Bruker GENOLINK software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000724 name: GenoTools def: "Bruker GenoTools software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000725 name: HCTcontrol def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000726 name: micrOTOFcontrol def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000727 name: PolyTools def: "Bruker PolyTools software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000728 name: ProfileAnalysis def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000729 name: PROTEINEER def: "Bruker PROTEINEER software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000730 name: PROTEINEER dp def: "Bruker PROTEINEER dp software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000731 name: PROTEINEER fc def: "Bruker PROTEINEER fc software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000732 name: PROTEINEER spII def: "Bruker PROTEINEER spII software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000733 name: PROTEINEER-LC def: "Bruker PROTEINEER-LC software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000734 name: ProteinScape def: "Bruker ProteinScape software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000735 name: PureDisk def: "BrukerPureDisk software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000736 name: QuantAnalysis def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000737 name: spControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000738 name: TargetAnalysis def: "Bruker TargetAnalysis software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000739 name: WARP-LC def: "Bruker WARP-LC software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000740 name: parameter file def: "Parameter file used to configure the acquisition of raw data on the instrument." [PSI:MS] is_a: MS:1000560 ! Source File Type [Term] id: MS:1000741 name: Conversion to dta def: "Conversion to dta format." [PSI:MS] is_a: MS:1000530 ! file format conversion [Term] id: MS:1000742 name: Bioworks SRF file def: "Thermo Finnigan SRF file format." [PSI:MS] is_a: MS:1000560 ! source file type [Term] id: MS:1000743 name: TSQ Quantum Ultra AM def: "Thermo Scientific TSQ Quantum Ultra AM." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000744 name: selected m/z def: "Mass-to-charge ratio of the ion selected for fragmentation" [PSI:MS] is_a: MS:1000455 ! ion selection attribute xref: value-type:xsd\:float "The allowed value-type for this CV term." relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000745 name: retention time alignment def: "The correction of the spectrum scan times, as used e.g. in label-free proteomics." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000746 name: high intensity data point removal def: "The removal of very high intensity data points." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000747 name: completion time def: "The time that a data processing action was finished." [PSI:MS] is_a: MS:1000630 ! data processing parameter xref: value-type:xsd\:date "The allowed value-type for this CV term." [Term] id: MS:1000748 name: SSQ 7000 def: "ThermoFinnigan SSQ 7000 MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000749 name: TSQ 7000 def: "ThermoFinnigan TSQ 7000 MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000750 name: TSQ def: "ThermoFinnigan TSQ MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000751 name: TSQ Quantum Ultra def: "Thermo Scientific TSQ Quantum Ultra." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000752 name: TOPP software def: "TOPP (The OpenMS proteomics pipeline) software." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000753 name: BaselineFilter def: "Removes the baseline from profile spectra using a top-hat filter." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000754 name: DBExporter def: "Exports data from an OpenMS database to a file." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000755 name: DBImporter def: "Imports data to an OpenMS database." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000756 name: FileConverter def: "Converts between different MS file formats." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000757 name: FileFilter def: "Extracts or manipulates portions of data from peak, feature or consensus feature files." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000758 name: FileMerger def: "Merges several MS files into one file." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000759 name: InternalCalibration def: "Applies an internal calibration." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000760 name: MapAligner def: "Corrects retention time distortions between maps." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000761 name: MapNormalizer def: "Normalizes peak intensities in an MS run." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000762 name: NoiseFilter def: "Removes noise from profile spectra by using different smoothing techniques." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000763 name: PeakPicker def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000764 name: Resampler def: "Transforms an LC/MS map into a resampled map or a png image." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000765 name: SpectraFilter def: "Applies a filter to peak spectra." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000766 name: TOFCalibration def: "Applies time of flight calibration." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000767 name: native spectrum identifier format def: "Describes how the native spectrum identifiers are formated." [PSI:MS] synonym: "nativeID format" EXACT [] relationship: part_of MS:1000577 ! data file [Term] id: MS:1000768 name: Thermo nativeID format def: "controller=xsd:nonNegativeInteger scan=xsd:positiveInteger." [PSI:MS] comment: controller=0 is usually the mass spectrometer is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000769 name: Waters nativeID format def: "function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000770 name: WIFF nativeID format def: "sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000771 name: Bruker/Agilent YEP nativeID format def: "scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000772 name: Bruker BAF nativeID format def: "scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000773 name: Bruker FID nativeID format def: "file=xsd:IDREF" [PSI:MS] comment: The nativeID must be the same as the source file ID. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000774 name: multiple peak list nativeID format def: "index=xsd:nonNegativeInteger" [PSI:MS] comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000775 name: single peak list nativeID format def: "file=xsd:IDREF" [PSI:MS] comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000776 name: scan number only nativeID format def: "scan=xsd:nonNegativeInteger" [PSI:MS] comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000777 name: spectrum identifier nativeID format def: "spectrum=xsd:nonNegativeInteger" [PSI:MS] comment: Used for conversion from mzData. The spectrum id attribute is referenced. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000778 name: charge state calculation def: "A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000779 name: below precursor intensity dominance charge state calculation def: "Infers charge state as single or amibiguously multiple by determining the fraction of intensity below the precursor m/z." [PSI:MS] is_a: MS:1000778 ! charge state calculation [Term] id: MS:1000780 name: precursor recalculation def: "A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000781 name: msPrefix precursor recalculation def: "Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans." [PSI:MS] is_a: MS:1000780 ! precursor recalculation [Term] id: MS:1000782 name: Savitzky-Golay smoothing def: "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." [PSI:MS] is_a: MS:1000592 ! smoothing [Term] id: MS:1000783 name: LOWESS smoothing def: "Reduces intensity spikes by applying a modeling 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." [PSI:MS] is_a: MS:1000592 ! smoothing [Term] id: MS:1000784 name: Gaussian smoothing def: "Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function." [PSI:MS] synonym: "Weierstrass transform" EXACT [] synonym: "binomial smoothing" EXACT [] is_a: MS:1000592 ! smoothing [Term] id: MS:1000785 name: moving average smoothing def: "Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect." [PSI:MS] synonym: "box smoothing" EXACT [] synonym: "boxcar smoothing" EXACT [] synonym: "sliding average smoothing" EXACT [] is_a: MS:1000592 ! smoothing [Term] id: MS:1000786 name: non-standard data array def: "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." [PSI:MS] is_a: MS:1000513 ! binary data array xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000787 name: inclusive low intensity threshold def: "Threshold at or below which some action is taken." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:1000788 name: inclusive high intensity threshold def: "Threshold at or above which some action is taken." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:1000789 name: enhanced multiply charged spectrum def: "MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions" [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000790 name: time-delayed fragmentation spectrum def: "MS2 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" [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000791 name: enhanced resolution scan def: "Scan with enhanced resolution." [PSI:MS] is_a: MS:1000020 ! scanning method [Term] id: MS:1000792 name: isolation window attribute def: "Isolation window parameter." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000441 ! scan [Term] id: MS:1000793 name: isolation m/z upper limit def: "The highest m/z being isolated in an isolation window." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000794 name: isolation m/z lower limit def: "The lowest m/z being isolated in an isolation window." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000795 name: no combination def: "Use this term if only one scan was recorded or there is no information about scans available." [PSI:MS] is_a: MS:1000570 ! spectra combination [Term] id: MS:1000796 name: spectrum title def: "A free-form text title describing a spectrum." [PSI:MS] comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list. This term corresponds to Protein Informatics CV term PI:00416 is_a: MS:1000499 ! spectrum attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000797 name: peak list scans def: "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." [PSI:MS] comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list. This term corresponds to Protein Informatics CV term PI:00414 is_a: MS:1000499 ! spectrum attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000798 name: peak list raw scans def: "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." [PSI:MS] comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list. This term corresponds to Protein Informatics CV term PI:00415 is_a: MS:1000499 ! spectrum attribute xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000799 name: custom unreleased software tool def: "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." [PSI:MS] is_a: MS:1000531 ! software xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS:1000800 name: mass resolving power def: "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." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute [Term] id: MS:1000801 name: area peak picking def: "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." [PSI:MS] synonym: "sum peak picking" EXACT [] is_a: MS:1000035 ! peak picking [Term] id: MS:1000802 name: height peak picking def: "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." [PSI:MS] synonym: "max peak picking" EXACT [] is_a: MS:1000035 ! peak picking [Typedef] id: has_units name: has_units [Typedef] id: part_of name: part_of is_transitive: true