format-version: 1.2

 data-version: 4.1.41
 date: 30:07:2020 18:25
 saved-by: Matt Chambers

 auto-generated-by: OBO-Edit 2.3.1
 import: http://ontologies.berkeleybop.org/pato.obo
 import: http://ontologies.berkeleybop.org/uo.obo

 default-namespace: MS

 namespace-id-rule: * MS:$sequence(7,0,9999999)$

 namespace-id-rule: * PEFF:$sequence(7,0,9999999)$

 remark: namespace: MS

 remark: namespace: PEFF

 remark: coverage: Mass spectrometer output files and spectra interpretation
 remark: creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu>
 remark: creator: Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de>
 remark: creator: Marius Kallhardt <Marius.Kallhardt <-at-> bdal.de>
 remark: creator: Eric Deutsch <edeutsch <-at-> systemsbiology.org>
 remark: creator: Fredrik Levander <fredrik.levander <-at-> immun.lth.se>

 remark: creator: Pierre-Alain Binz <pierre-alain.binz <-at-> chuv.ch>

 remark: creator: Gerhard Mayer <mayerg97 <-at-> rub.de>
 remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics 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 and http://mass-spec.lsu.edu/msterms/index.php/Main_Page

 remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net

 remark: URL: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

 remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
 remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.

 ontology: ms

 
 [Typedef]
 id: has_regexp
 name: has regexp
 
 [Typedef]
 id: has_units
 name: has_units
 
 [Typedef]
 id: part_of
 name: part_of
 is_transitive: true
 
 [Typedef]
 id: has_order
 name: has_order
 
 [Typedef]
 id: has_domain
 name: has_domain

 
 [Term]
 id: MS:0000000
 name: Proteomics Standards Initiative Mass Spectrometry Vocabularies
 def: "Proteomics Standards Initiative Mass Spectrometry Vocabularies." [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]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000548 ! sample attribute

 
 [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:0000021 ! gram
 
 [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:0000098 ! milliliter
 
 [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:0000175 ! gram per liter
 
 [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: "OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer." [PSI:MS]

 comment: This term was made obsolete because it was replaced by scan polarity (MS:1000465).

 is_obsolete: true
 
 [Term]
 id: MS:1000010
 name: analyzer type

 def: "OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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: "OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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 MS:1000040 ! m/z
 relationship: has_units UO:0000169 ! parts per million
 
 [Term]
 id: MS:1000015
 name: scan rate
 def: "Rate in Th/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
 relationship: has_units MS:1000807 ! Th/s
 
 [Term]
 id: MS:1000016
 name: scan start time
 def: "The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000503 ! scan attribute

 is_a: MS:1002345 ! PSM-level attribute

 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute
 
 [Term]
 id: MS:1000017
 name: Scan Function

 def: "OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum." [PSI:MS]
 comment: OBSOLETE This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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]

 comment: OBSOLETE This former purgatory term was made obsolete.

 synonym: "Tandem Scanning Method" RELATED []

 is_obsolete: true

 
 [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:0000008 ! meter
 
 [Term]
 id: MS:1000023
 name: isolation width

 def: "OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion." [PSI:MS]
 comment: This former purgatory term was made obsolete.

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 relationship: has_units MS:1000040 ! m/z

 is_obsolete: true

 
 [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]
 synonym: "B" EXACT []
 synonym: "Magnetic Field" RELATED []
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000480 ! mass analyzer attribute
 relationship: has_units UO:0000228 ! tesla
 
 [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]
 synonym: "ADC Sampling Frequency" NARROW []
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000481 ! detector attribute
 relationship: has_units UO:0000106 ! hertz
 
 [Term]
 id: MS:1000030
 name: vendor

 def: "OBSOLETE Name of instrument vendor." [PSI:MS]
 comment: This term was made obsolete because it was replaced by instrument model (MS:1000031).

 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: "OBSOLETE." [PSI:MS]
 comment: This term was made obsolete because .

 is_obsolete: true
 
 [Term]
 id: MS:1000037
 name: polarity

 def: "OBSOLETE Terms to describe the polarity setting of the instrument." [PSI:MS]
 comment: This term was made obsolete because it was redundant with the Pato Ontology term polarity (UO:0002186).
 is_obsolete: true

 
 [Term]
 id: MS:1000038
 name: minute
 def: "OBSOLETE Acquisition time in minutes." [PSI:MS]

 comment: This term was made obsolete because it was redundant with Unit Ontology minute (UO:0000031).

 is_obsolete: true
 
 [Term]
 id: MS:1000039
 name: second
 def: "OBSOLETE Acquisition time in seconds." [PSI:MS]

 comment: This term was made obsolete because it was redundant with Unit Ontology second (UO:0000010).

 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: UO:0000000 ! unit

 
 [Term]
 id: MS:1000041
 name: charge state

 def: "Number of net charges, positive or negative, on an ion." [PSI:MS]

 synonym: "z" EXACT []

 xref: value-type:xsd\:int "The allowed value-type for this CV term."
 is_a: MS:1000455 ! ion selection attribute

 is_a: MS:1000507 ! ion property

 
 [Term]
 id: MS:1000042
 name: peak 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

 relationship: has_units MS:1000131 ! number of detector counts

 relationship: has_units MS:1000132 ! percent of base peak
 relationship: has_units MS:1000814 ! counts per second

 relationship: has_units MS:1000905 ! percent of base peak times 100

 relationship: has_units UO:0000269 ! absorbance unit
 relationship: part_of MS:1000231 ! peak
 
 [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: UO:0000000 ! 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:0000266 ! electronvolt
 
 [Term]
 id: MS:1000046
 name: energy unit
 def: "OBSOLETE Energy units are represented in either eV or Joules." [PSI:MS]

 comment: This term was made obsolete because it was redundant with the Unit Ontology term energy unit (UO:0000111).
 is_a: UO:0000000 ! 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: gaseous sample state

 def: "State if the sample is in gaseous form." [PSI:MS]
 is_a: MS:1000003 ! sample state
 
 [Term]
 id: MS:1000049

 name: liquid sample state

 def: "State if the sample is in liquid form." [PSI:MS]
 is_a: MS:1000003 ! sample state
 
 [Term]
 id: MS:1000050

 name: solid sample state

 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]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000548 ! sample attribute
 
 [Term]
 id: MS:1000054
 name: chromatography

 def: "OBSOLETE Chromatographic conditions used to obtain the sample." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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 ion source 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 ion source 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 entrance to the vacuum 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: "OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended." [PSI:MS]
 comment: This term was made obsolete because it was replaced by electron ionization (MS:1000389).

 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: "OBSOLETE." [PSI:MS]
 comment: This term was made obsolete because it was replaced by negative scan (MS:1000129).

 is_obsolete: true
 
 [Term]
 id: MS:1000077
 name: positive ion mode

 def: "OBSOLETE." [PSI:MS]
 comment: This term was made obsolete because it was replaced by positive scan (MS:1000130).

 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:1000291 ! linear 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:1000291 ! linear 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: "OBSOLETE When resolution is constant with respect to m/z." [PSI:MS]
 comment: This child of the former purgatory term resolution type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000089
 name: proportional

 def: "OBSOLETE When resolution is proportional with respect to m/z." [PSI:MS]
 comment: This child of the former purgatory term resolution type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000090
 name: mass scan

 def: "OBSOLETE A variation of instrument where a selected mass is scanned." [PSI:MS]
 comment: This child of the former purgatory term Scan Function was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000091
 name: selected ion detection

 def: "OBSOLETE Please see Single Ion Monitoring." [PSI:MS]
 comment: This child of the former purgatory term Scan Function was made obsolete.
 is_obsolete: true

 
 [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: "OBSOLETE The mass scan is done in linear mode." [PSI:MS]
 comment: This term was made obsolete because it was redundant with the Pato Ontology term linear (UO:0001199).

 is_a: MS:1000019 ! scan law

 is_obsolete: true

 
 [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: "OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000098
 name: multiple ion monitoring

 def: "OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000099
 name: multiple reaction monitoring
 def: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS]

 comment: This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206).

 synonym: "MRM" EXACT []
 is_obsolete: true
 
 [Term]
 id: MS:1000100
 name: precursor ion scan

 def: "OBSOLETE The specific scan function or process that will record a precursor ion spectrum." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000101
 name: product ion scan

 def: "OBSOLETE The specific scan function or process that records product ion spectrum." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000102
 name: single ion monitoring
 def: "OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum." [PSI:MS]

 comment: This term was made obsolete because it was replaced by single ion monitoring (MS:100205).

 is_obsolete: true
 
 [Term]
 id: MS:1000103
 name: single reaction monitoring
 def: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS]

 comment: This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206).

 is_obsolete: true
 
 [Term]
 id: MS:1000104

 name: None ??

 def: "OBSOLETE None." [PSI:MS]

 comment: This term was made obsolete because .

 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:1000345 ! array detector

 
 [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: 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 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 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:1000465 ! scan polarity

 is_a: MS:1000808 ! chromatogram attribute

 
 [Term]
 id: MS:1000130
 name: positive scan
 def: "Polarity of the scan is positive." [PSI:MS]
 is_a: MS:1000465 ! scan polarity

 is_a: MS:1000808 ! chromatogram attribute

 
 [Term]
 id: MS:1000131

 name: number of detector 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 []

 synonym: "CAD" EXACT []

 synonym: "collisionally activated dissociation" 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: "OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J." [PSI:MS]

 comment: This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266).

 is_obsolete: true
 
 [Term]
 id: MS:1000138

 name: normalized collision energy
 def: "Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions." [PSI:PI]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000510 ! precursor activation attribute

 relationship: has_units UO:0000187 ! percent

 
 [Term]
 id: MS:1000139

 name: 4000 QTRAP

 def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS." [PSI:MS]

 is_a: MS:1000121 ! 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: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS]
 is_a: MS:1001556 ! Bruker Daltonics apex series
 
 [Term]
 id: MS:1000142
 name: apex Q
 def: "Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS]
 is_a: MS:1001556 ! Bruker Daltonics apex series
 
 [Term]
 id: MS:1000143
 name: API 150EX
 def: "Applied Biosystems/MDS SCIEX API 150EX MS." [PSI:MS]

 is_a: MS:1000121 ! 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 ! SCIEX instrument model

 
 [Term]
 id: MS:1000145
 name: API 2000
 def: "Applied Biosystems/MDS SCIEX API 2000 MS." [PSI:MS]

 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000146
 name: API 3000
 def: "Applied Biosystems/MDS SCIEX API 3000 MS." [PSI:MS]

 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000147
 name: API 4000
 def: "Applied Biosystems/MDS SCIEX API 4000 MS." [PSI:MS]

 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000148
 name: autoflex II
 def: "Bruker Daltonics' autoflex II: MALDI TOF." [PSI:MS]
 is_a: MS:1001534 ! Bruker Daltonics flex series
 
 [Term]
 id: MS:1000149
 name: autoflex TOF/TOF
 def: "Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF." [PSI:MS]
 is_a: MS:1001534 ! Bruker Daltonics flex series
 
 [Term]
 id: MS:1000150
 name: Auto Spec Ultima NT

 def: "Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model
 
 [Term]
 id: MS:1000151
 name: BioTOF II
 def: "Bruker Daltonics' BioTOF II: ESI TOF." [PSI:MS]
 is_a: MS:1001535 ! Bruker Daltonics BioTOF series
 
 [Term]
 id: MS:1000152
 name: BioTOF-Q
 def: "Bruker Daltonics' BioTOF-Q: ESI Q-TOF." [PSI:MS]
 is_a: MS:1001535 ! Bruker Daltonics BioTOF series
 
 [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: "OBSOLETE ThermoFinnigan ELEMENT2 MS." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000156
 name: esquire 4000
 def: "Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS]
 is_a: MS:1001533 ! Bruker Daltonics esquire series
 
 [Term]
 id: MS:1000157
 name: esquire 6000
 def: "Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS]
 is_a: MS:1001533 ! Bruker Daltonics esquire series
 
 [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 oa-ToF based GCT." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model
 
 [Term]
 id: MS:1000160
 name: HCT
 def: "Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS]

 is_a: MS:1000697 ! Bruker Daltonics HCT Series

 
 [Term]
 id: MS:1000161
 name: HCTplus
 def: "Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS]

 is_a: MS:1000697 ! Bruker Daltonics HCT Series

 
 [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 oa-ToF based MALDI L." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model
 
 [Term]
 id: MS:1000171
 name: M@LDI LR

 def: "Waters oa-ToF based MALDI LR." [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: MALDI TOF." [PSI:MS]
 is_a: MS:1001534 ! Bruker Daltonics flex series
 
 [Term]
 id: MS:1000178
 name: microTOF LC
 def: "Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI." [PSI:MS]
 is_a: MS:1001536 ! Bruker Daltonics micrOTOF series
 
 [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' OmniFlex: MALDI TOF." [PSI:MS]
 is_a: MS:1001534 ! Bruker Daltonics flex series
 
 [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 ! SCIEX instrument model

 
 [Term]
 id: MS:1000187
 name: Q TRAP
 def: "Applied Biosystems/MDS SCIEX Q TRAP MS." [PSI:MS]

 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000188
 name: Q-Tof micro

 def: "Waters oa-ToF based Q-Tof micro." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model
 
 [Term]
 id: MS:1000189

 name: Q-Tof Ultima

 def: "Waters oa-ToF based Q-Tof Ultima." [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 ! SCIEX instrument model

 
 [Term]
 id: MS:1000191
 name: quattro micro

 def: "Waters (triple) quadrupole based micro." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model
 
 [Term]
 id: MS:1000192

 name: Quattro Ultima
 def: "Waters (triple) quadrupole based Ultima." [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 ! SCIEX instrument model

 
 [Term]
 id: MS:1000195
 name: SymBiot XVI
 def: "Applied Biosystems/MDS SCIEX SymBiot XVI MS." [PSI:MS]

 is_a: MS:1000121 ! 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: MALDI TOF." [PSI:MS]
 is_a: MS:1001534 ! Bruker Daltonics flex series
 
 [Term]
 id: MS:1000202
 name: ultraflex TOF/TOF
 def: "Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF." [PSI:MS]
 is_a: MS:1001534 ! Bruker Daltonics flex series
 
 [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:1000596 ! measurement method

 
 [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:1000596 ! measurement method

 
 [Term]
 id: MS:1000207
 name: accurate mass

 def: "OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition." [PSI:MS]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 comment: This child of the former purgatory term ion attribute was made obsolete.

 relationship: has_units UO:0000002 ! mass unit

 is_obsolete: true

 
 [Term]
 id: MS:1000208
 name: average mass

 def: "OBSOLETE 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."

 comment: This child of the former purgatory term ion attribute was made obsolete.

 relationship: has_units UO:0000002 ! mass unit

 is_obsolete: true

 
 [Term]
 id: MS:1000209
 name: appearance energy

 def: "OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended." [PSI:MS]

 synonym: "AE" EXACT []
 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 comment: This child of the former purgatory term ion attribute was made obsolete.

 relationship: has_units UO:0000266 ! electronvolt

 is_obsolete: true

 
 [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: OBSOLETE charge number

 def: "OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state." [PSI:MS]

 xref: value-type:xsd\:int "The allowed value-type for this CV term."
 is_obsolete: true
 
 [Term]
 id: MS:1000212
 name: dalton
 def: "OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg." [PSI:MS]

 comment: This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221).

 is_obsolete: true
 
 [Term]
 id: MS:1000213
 name: electron affinity

 def: "OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy." [PSI:MS]
 comment: This child of the former purgatory term ion attribute was made obsolete.

 synonym: "EA" EXACT []
 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 is_obsolete: true

 
 [Term]
 id: MS:1000214
 name: electron energy obsolete

 def: "OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000215
 name: exact mass

 def: "OBSOLETE 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."

 comment: This child of the former purgatory term ion attribute was made obsolete.

 relationship: has_units UO:0000002 ! mass unit

 is_obsolete: true

 
 [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: "OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000218

 name: ionization efficiency

 def: "OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS]

 comment: This term was made obsolete because it was replaced by ionization efficiency (MS:1000392).

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_obsolete: true
 
 [Term]
 id: MS:1000219
 name: ionization energy

 def: "OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion." [PSI:MS]

 synonym: "IE" EXACT []

 comment: This child of the former purgatory term ion attribute was made obsolete.

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 relationship: has_units UO:0000266 ! electronvolt

 is_obsolete: true

 
 [Term]
 id: MS:1000220
 name: isotope dilution mass spectrometry

 def: "OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometry was made obsolete.

 synonym: "IDMS" EXACT []

 is_obsolete: true

 
 [Term]
 id: MS:1000221
 name: magnetic deflection

 def: "The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer." [PSI:MS]

 is_a: MS:1000597 ! ion optics type
 
 [Term]
 id: MS:1000222
 name: mass defect

 def: "OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom." [PSI:MS]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 comment: This child of the former purgatory term ion attribute was made obsolete.

 relationship: has_units UO:0000002 ! mass unit

 is_obsolete: true

 
 [Term]
 id: MS:1000223
 name: mass number

 def: "OBSOLETE 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."

 comment: This child of the former purgatory term ion attribute was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000224
 name: molecular mass

 def: "Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 is_a: MS:1000861 ! molecular entity property

 relationship: has_units UO:0000002 ! mass unit
 
 [Term]
 id: MS:1000225
 name: monoisotopic mass

 def: "OBSOLETE 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."

 comment: This child of the former purgatory term ion attribute was made obsolete.

 relationship: has_units UO:0000002 ! mass unit

 is_obsolete: true

 
 [Term]
 id: MS:1000226
 name: molecular beam mass spectrometry

 def: "OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.

 synonym: "MBMS" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000229
 name: nominal mass

 def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value." [PSI:MS]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 comment: This child of the former purgatory term ion attribute was made obsolete.

 relationship: has_units UO:0000002 ! mass unit

 is_obsolete: true

 
 [Term]
 id: MS:1000230
 name: odd-electron rule

 def: "OBSOLETE 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]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [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:1000442 ! spectrum
 
 [Term]
 id: MS:1000232
 name: peak intensity
 def: "OBSOLETE The height or area of a peak in a mass spectrum." [PSI:MS]

 comment: This term was made obsolete because it was replaced by base peak intensity (MS:1000505).

 is_obsolete: true
 
 [Term]
 id: MS:1000233
 name: proton affinity

 def: "OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states." [PSI:MS]

 synonym: "PA" EXACT [PSI:MS]

 comment: This child of the former purgatory term ion attribute was made obsolete.

 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 is_obsolete: true

 
 [Term]
 id: MS:1000234
 name: mass resolving power
 def: "OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported." [PSI:MS]

 comment: This term was made obsolete because it was replaced by mass resolving power (MS:1000800).

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_obsolete: true
 
 [Term]
 id: MS:1000235
 name: total ion current chromatogram

 def: "Representation of the total ion current detected in each of a series of mass spectra versus time." [PSI:MS]

 synonym: "TIC chromatogram" EXACT []

 is_a: MS:1000810 ! ion current chromatogram

 
 [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: "OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg." [PSI:MS]

 comment: This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221).

 synonym: "u" EXACT []
 is_obsolete: true
 
 [Term]
 id: MS:1000238
 name: accelerator mass spectrometry

 def: "OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.

 synonym: "AMS" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS]

 comment: This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382).

 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
 
 [Term]
 id: MS:1000243
 name: charge-remote fragmentation

 def: "OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.

 synonym: "CRF" EXACT []

 is_obsolete: true

 
 [Term]
 id: MS:1000244
 name: consecutive reaction monitoring

 def: "OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS]
 comment: This former purgatory term was made obsolete.

 synonym: "CRM" EXACT []

 is_obsolete: true

 
 [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
 
 [Term]
 id: MS:1000251
 name: even-electron ion

 def: "OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.

 synonym: "EE" EXACT []

 is_obsolete: true

 
 [Term]
 id: MS:1000252
 name: electron-induced excitation in organics

 def: "OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.

 synonym: "EIEIO" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.

 synonym: "FAIMS" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.

 synonym: "IKES" EXACT []

 is_obsolete: true

 
 [Term]
 id: MS:1000261
 name: ion mobility spectrometry

 def: "OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.

 synonym: "IMS" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometry was made obsolete.

 synonym: "IRMS" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.

 synonym: "KERD" EXACT []

 is_obsolete: true

 
 [Term]
 id: MS:1000266
 name: Laser Desorption

 alt_id: MS:1000393

 def: "OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules." [PSI:MS]

 comment: This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393).

 synonym: "Laser Ionization MERGE" EXACT []
 synonym: "LD" EXACT []
 is_obsolete: true
 
 [Term]
 id: MS:1000267
 name: mass analyzed ion kinetic energy spectrometry

 def: "OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.

 synonym: "MIKES" EXACT []

 is_obsolete: true

 
 [Term]
 id: MS:1000268
 name: mass spectrometry

 def: "OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments." [PSI:MS]
 comment: This former purgatory term was made obsolete.

 synonym: "MS" EXACT []

 is_obsolete: true

 
 [Term]
 id: MS:1000269
 name: mass spectrometry/mass spectrometry

 def: "OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.

 synonym: "MS/MS" EXACT []

 is_obsolete: true

 
 [Term]
 id: MS:1000270
 name: multiple stage mass spectrometry

 def: "OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.

 synonym: "MSn" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.

 synonym: "RGA" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS]

 comment: This term was made obsolete because it was replaced by surface ionization (MS:1000406).

 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: "OBSOLETE Mass spectrometry using spark ionization." [PSI:MS]

 comment: This term was made obsolete because it was replaced by spark ionization (MS:1000404).

 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 MS2 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 []
 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 is_a: MS:1003058 ! spectrum property

 
 [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: "OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.

 synonym: "TOF-MS" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE 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]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000290
 name: hybrid mass spectrometer

 def: "OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.
 is_obsolete: true

 
 [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: "OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000293
 name: mass spectrometer

 def: "OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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:1000524 ! data file content
 is_a: MS:1000559 ! spectrum type
 
 [Term]
 id: MS:1000295
 name: mattauch-herzog geometry

 def: "OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000296
 name: nier-johnson geometry

 def: "OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000297
 name: paul ion trap

 def: "OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected." [PSI:MS]
 comment: This term was made obsolete because it is redundant to quadrupole ion trap.

 synonym: "quadrupole ion trap" RELATED []

 is_obsolete: true

 
 [Term]
 id: MS:1000298
 name: prolate traochoidal mass spectrometer

 def: "OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000299
 name: quistor

 def: "OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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: "OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000302
 name: tandem mass spectrometer

 def: "OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000303
 name: transmission quadrupole mass spectrometer

 def: "OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.
 is_obsolete: true

 
 [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:0000218 ! volt
 
 [Term]
 id: MS:1000305
 name: cyclotron motion

 def: "OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000306
 name: dynamic mass spectrometry

 def: "OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time." [PSI:MS]
 comment: This child of the former purgatory term mass spectrometer was made obsolete.
 is_obsolete: true

 
 [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]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000487 ! ion optics attribute
 relationship: has_units UO:0000268 ! volt per meter
 
 [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: "OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000313
 name: scan m/z range?

 def: "OBSOLETE The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000314
 name: mass selective axial ejection

 def: "OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000315
 name: mass selective instability

 def: "OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000316
 name: mathieu stability diagram

 def: "OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000317
 name: orthogonal extraction

 def: "OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000318
 name: resonance ion ejection

 def: "OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.
 is_obsolete: true

 
 [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: "OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.
 is_obsolete: true

 
 [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: "OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement." [PSI:MS]
 comment: This former purgatory term was made obsolete.

 synonym: "constant neutral mass loss scan" RELATED []
 synonym: "fixed neutral fragment scan" RELATED []

 is_obsolete: true

 
 [Term]
 id: MS:1000324
 name: constant neutral gain scan

 def: "OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment." [PSI:MS]
 comment: This former purgatory term was made obsolete.

 synonym: "Constant Neutral Mass Gain Scan" EXACT []

 is_obsolete: true

 
 [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:1000294 ! mass spectrum
 
 [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:1000294 ! mass spectrum
 
 [Term]
 id: MS:1000327
 name: consecutive reaction monitoring

 def: "OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS]

 comment: This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244).

 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: "OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000330
 name: linked scan at constant b/e

 def: "OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors." [PSI:MS]
 comment: This child of the former purgatory term linked scan was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000331
 name: Linked Scan at Constant E2/V

 def: "OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors." [PSI:MS]
 comment: This child of the former purgatory term linked scan was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000332
 name: Linked Scan at Constant B2/E

 def: "OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended." [PSI:MS]
 comment: This child of the former purgatory term linked scan was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000333
 name: Linked Scan at Constant B[1-(E/E0)]^1/2 / E

 def: "OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan." [PSI:MS]
 comment: This child of the former purgatory term linked scan was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000334
 name: MS/MS in Time

 def: "OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000335
 name: MS/MS in Space

 def: "OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition." [PSI:MS]
 comment: This child of the former purgatory term m/z Separation Method was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000336
 name: neutral loss

 def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1001055 ! modification parameters
 
 [Term]
 id: MS:1000337
 name: nth generation product ion

 def: "OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated." [PSI:MS]
 comment: This child of the former purgatory term product ion was made obsolete.

 synonym: "granddaughter ion" RELATED []

 is_obsolete: true

 
 [Term]
 id: MS:1000338
 name: nth generation product ion scan

 def: "OBSOLETE 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]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000339
 name: nth generation product ion spectrum
 def: "OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions." [PSI:MS]

 comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580).

 is_obsolete: true
 
 [Term]
 id: MS:1000340
 name: precursor ion

 def: "OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated." [PSI:MS]
 comment: This child of the former purgatory term ion role was made obsolete.

 synonym: "parent ion" RELATED []

 is_obsolete: true

 
 [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:1000294 ! mass spectrum
 
 [Term]
 id: MS:1000342
 name: product ion

 def: "OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated." [PSI:MS]
 comment: This child of the former purgatory term ion role was made obsolete.

 synonym: "daughter ion" RELATED []

 is_obsolete: true

 
 [Term]
 id: MS:1000343
 name: product ion spectrum
 def: "OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions." [PSI:MS]

 comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580).

 is_a: MS:1000294 ! mass spectrum
 is_obsolete: true
 
 [Term]
 id: MS:1000344
 name: progeny ion

 def: "OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.

 synonym: "Progeny Fragment Ion" EXACT []

 is_obsolete: true

 
 [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: "OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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:1003055 ! adduct

 
 [Term]
 id: MS:1000354
 name: aromatic ion

 def: "OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000355
 name: analog ion

 def: "OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000356
 name: anti-aromatic ion

 def: "OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000357
 name: cationized molecule

 def: "OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000358
 name: cluster ion

 def: "OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000359
 name: Conventional ion

 def: "OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000360
 name: diagnostic ion

 def: "OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000361
 name: dimeric ion

 def: "OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000362
 name: distonic ion

 def: "OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000363
 name: enium ion

 def: "OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000364
 name: fragment ion
 def: "OBSOLETE A product ion that results from the dissociation of a precursor ion." [PSI:MS]

 comment: This term was made obsolete because it was replaced by product ion (MS:1000342).

 is_obsolete: true
 
 [Term]
 id: MS:1000365
 name: ion?

 def: "OBSOLETE An atomic or molecular species having a net positive or negative electric charge." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000366
 name: Isotopologue ion

 def: "OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000367
 name: Isotopomeric ion

 def: "OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000368
 name: metastable ion

 def: "OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection." [PSI:MS]
 comment: This child of the former purgatory term ion stability type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000369
 name: molecular ion

 def: "OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000370
 name: negative ion

 def: "OBSOLETE An atomic or molecular species having a net negative electric charge." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000371
 name: non-classical ion

 def: "OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000372
 name: onium ion

 def: "OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000373
 name: principal ion

 def: "OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000374
 name: positive ion

 def: "OBSOLETE An atomic or molecular species having a net positive electric charge." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000375
 name: protonated molecule

 def: "OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000376
 name: radical ion

 def: "OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000377
 name: reference ion

 def: "OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion." [PSI:MS]
 comment: This child of the former purgatory term ion chemical type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000378
 name: stable ion

 def: "OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer." [PSI:MS]
 comment: This child of the former purgatory term ion stability type was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000379
 name: unstable ion

 def: "OBSOLETE An ion with sufficient energy to dissociate within the ion source." [PSI:MS]
 comment: This child of the former purgatory term ion stability type was made obsolete.
 is_obsolete: true

 
 [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 discrete 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: "OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000391
 name: ion-pair formation

 def: "OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [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 nanoelectrospray." [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: "OBSOLETE An electronic state capable of undergoing auto-Ionization." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [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: "OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000410
 name: alpha-cleavage

 def: "OBSOLETE 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]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000411
 name: beta-cleavage

 def: "OBSOLETE 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]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000412
 name: buffer gas
 def: "An inert gas used for collisional deactivation of internally excited ions." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000510 ! precursor activation attribute
 
 [Term]
 id: MS:1000413
 name: charge-induced fragmentation

 def: "OBSOLETE 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]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000414
 name: charge inversion reaction

 def: "OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000415
 name: charge permutation reaction

 def: "OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000416
 name: charge stripping reaction

 def: "OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000417
 name: charge transfer reaction

 def: "OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000418
 name: collisional excitation

 def: "OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000419
 name: collision gas
 def: "An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000510 ! precursor activation attribute
 
 [Term]
 id: MS:1000420
 name: heterolytic cleavage

 def: "OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.

 synonym: "heterolysis" RELATED []

 is_obsolete: true

 
 [Term]
 id: MS:1000421
 name: high energy collision

 def: "OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000422

 name: beam-type collision-induced dissociation
 def: "A collision-induced dissociation process that occurs in a beam-type collision cell." [PSI:MS]

 synonym: "HCD" EXACT []

 is_a: MS:1000133 ! collision-induced dissociation

 
 [Term]
 id: MS:1000423
 name: homolytic cleavage

 def: "OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.

 synonym: "homolysis" RELATED []

 is_obsolete: true

 
 [Term]
 id: MS:1000424
 name: hydrogen/deuterium exchange

 def: "OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000425
 name: ion energy loss spectrum

 def: "OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000426
 name: ionizing collision

 def: "OBSOLETE 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]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000427
 name: ion/molecule reaction

 def: "OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000428
 name: ion/neutral complex

 def: "OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000429
 name: ion/neutral species reaction

 def: "OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000430
 name: ion/neutral species exchange reaction

 def: "OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000431
 name: kinetic method

 def: "OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000432
 name: low energy collisions

 def: "OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [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: "OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [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 []
 synonym: "MPD" EXACT []

 is_a: MS:1000044 ! dissociation method
 
 [Term]
 id: MS:1000436
 name: partial charge transfer reaction

 def: "OBSOLETE 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]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000437
 name: ion reaction

 def: "OBSOLETE Chemical transformation involving an ion." [PSI:MS]

 comment: This child of the former purgatory term ion was made obsolete.

 is_obsolete: true

 
 [Term]
 id: MS:1000438
 name: superelastic collision

 def: "OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000439
 name: surface-induced reaction

 def: "OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000440
 name: unimolecular dissociation

 def: "OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion." [PSI:MS]
 comment: This child of the former purgatory term ion reaction was made obsolete.
 is_obsolete: true

 
 [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:1001458 ! spectrum generation information
 
 [Term]
 id: MS:1000442
 name: spectrum

 def: "Representation of intensity values corresponding to a range of measurement space." [PSI:MS]

 relationship: part_of MS:1001458 ! spectrum generation information
 
 [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: "OBSOLETE Mass/charge separation Method." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000445

 name: sequential m/z separation method

 def: "OBSOLETE Sequential m/z separation method." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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]
 synonym: "analyzer" EXACT []
 relationship: part_of MS:1000463 ! instrument
 
 [Term]
 id: MS:1000452
 name: data transformation
 def: "Terms used to describe types of data processing." [PSI:MS]
 synonym: "data processing" EXACT []
 relationship: part_of MS:1001458 ! spectrum generation information
 
 [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: "OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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]
 synonym: "activation" EXACT []
 relationship: part_of MS:1000442 ! spectrum
 
 [Term]
 id: MS:1000457
 name: sample
 def: "Terms to describe the sample." [PSI:MS]
 relationship: part_of MS:1001458 ! spectrum generation information
 
 [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: "OBSOLETE Terms used to describe the spectrum." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000460
 name: unit

 def: "OBSOLETE Terms to describe units." [PSI:MS]
 comment: This term was made obsolete because it was redundant with the Unit Ontology term unit (UO:0000000).

 relationship: part_of MS:1001458 ! spectrum generation information

 is_obsolete: true

 
 [Term]
 id: MS:1000461
 name: additional description

 def: "OBSOLETE Terms to describe Additional." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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]
 synonym: "instrument configuration" EXACT []
 relationship: part_of MS:1001458 ! spectrum generation information
 
 [Term]
 id: MS:1000464
 name: mass unit
 def: "OBSOLETE A unit of measurement for mass." [PSI:MS]

 comment: This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002).

 is_obsolete: true
 
 [Term]
 id: MS:1000465
 name: scan polarity

 def: "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS]

 relationship: part_of MS:1000441 ! scan
 
 [Term]
 id: MS:1000466
 name: alternating
 def: "OBSOLETE Alternating." [PSI:MS]

 comment: This term was made obsolete because .

 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 MS2 and 11 stages of manual MS2." [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: 6120A Quadrupole LC/MS
 def: "The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition." [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: "OBSOLETE Terms that will likely become obsolete unless there are wails of dissent." [PSI:MS]
 comment: The whole branch purgatory term was made obsolete.
 is_obsolete: true

 
 [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:0000218 ! volt
 
 [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 resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS]

 synonym: "enhanced resolution scan" EXACT []

 is_a: MS:1000503 ! scan attribute

 
 [Term]
 id: MS:1000498
 name: full scan

 def: "OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [Term]
 id: MS:1000499
 name: spectrum attribute

 def: "Nonphysical characteristic attributed to a spectrum." [PSI:MS]

 relationship: part_of MS:1000442 ! spectrum
 
 [Term]
 id: MS:1000500
 name: scan window upper limit
 def: "The lower m/z bound of a mass spectrometer scan window." [PSI:MS]
 synonym: "mzRangeStop" RELATED []
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000549 ! selection window attribute
 relationship: has_units MS:1000040 ! m/z
 
 [Term]
 id: MS:1000501
 name: scan window lower limit
 def: "The upper m/z bound of a mass spectrometer scan window." [PSI:MS]
 synonym: "mzRangeStart" RELATED []
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 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]
 synonym: "Scan Duration" RELATED []
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000503 ! scan attribute
 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute
 
 [Term]
 id: MS:1000503
 name: scan attribute

 def: "Nonphysical characteristic attributed to a spectrum acquisition scan." [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 signal of highest intensity in the mass spectrum." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 is_a: MS:1003058 ! spectrum property

 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:1003058 ! spectrum property

 relationship: has_units MS:1000131 ! number of detector counts

 relationship: has_units MS:1000132 ! percent of base peak
 relationship: has_units MS:1000814 ! counts per second
 relationship: has_units MS:1000905 ! percent of base peak times 100
 relationship: has_units UO:0000269 ! absorbance unit
 
 [Term]
 id: MS:1000506
 name: ion role

 def: "OBSOLETE Ion Role." [PSI:MS]

 comment: This child of the former purgatory term ion was made obsolete.

 is_obsolete: true

 
 [Term]
 id: MS:1000507

 name: ion property
 def: "Nonphysical characteristic attributed to an ion." [PSI:MS]
 relationship: part_of MS:1002806 ! ion

 
 [Term]
 id: MS:1000508
 name: ion chemical type

 def: "OBSOLETE Ion Type." [PSI:MS]

 comment: This child of the former purgatory term ion was made obsolete.

 is_obsolete: true

 
 [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:0000266 ! electronvolt
 
 [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: "Stage number achieved in a multi stage mass spectrometry acquisition." [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 m/z values." [PSI:MS]

 xref: binary-data-type:MS\:1000521 "32-bit float"
 xref: binary-data-type:MS\:1000523 "64-bit float"

 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]

 xref: binary-data-type:MS\:1000521 "32-bit float"
 xref: binary-data-type:MS\:1000523 "64-bit float"

 is_a: MS:1000513 ! binary data array

 relationship: has_units MS:1000131 ! number of detector counts

 relationship: has_units MS:1000132 ! percent of base peak
 relationship: has_units MS:1000814 ! counts per second
 relationship: has_units MS:1000905 ! percent of base peak times 100
 relationship: has_units UO:0000269 ! absorbance unit
 
 [Term]
 id: MS:1000516
 name: charge array
 def: "A data array of charge values." [PSI:MS]

 xref: binary-data-type:MS\:1000519 "32-bit integer"

 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]

 xref: binary-data-type:MS\:1000521 "32-bit float"
 xref: binary-data-type:MS\:1000523 "64-bit float"

 is_a: MS:1000513 ! binary data array
 
 [Term]
 id: MS:1000518
 name: binary data type
 def: "Encoding type of binary data specifying the binary representation and precision, e.g. 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 little-endian integer." [PSI:MS]
 is_a: MS:1000518 ! binary data type
 
 [Term]
 id: MS:1000520
 name: 16-bit float
 def: "OBSOLETE Signed 16-bit float." [PSI:MS]
 is_a: MS:1000518 ! binary data type
 is_obsolete: true
 
 [Term]
 id: MS:1000521
 name: 32-bit float
 def: "32-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS]
 is_a: MS:1000518 ! binary data type
 
 [Term]
 id: MS:1000522
 name: 64-bit integer
 def: "Signed 64-bit little-endian integer." [PSI:MS]
 is_a: MS:1000518 ! binary data type
 
 [Term]
 id: MS:1000523
 name: 64-bit float
 def: "64-bit precision little-endian floating point conforming to 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 ! source 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: Waters raw format
 def: "Waters data file format found in a Waters RAW directory, generated from an MS acquisition." [PSI:MS]

 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000527
 name: highest observed m/z
 def: "Highest m/z value observed in the m/z array." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000808 ! chromatogram attribute

 is_a: MS:1003058 ! spectrum property

 relationship: has_units MS:1000040 ! m/z
 
 [Term]
 id: MS:1000528
 name: lowest observed m/z
 def: "Lowest m/z value observed in the m/z array." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000808 ! chromatogram attribute

 is_a: MS:1003058 ! spectrum property

 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 Vocabularies
 
 [Term]
 id: MS:1000532
 name: Xcalibur
 def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS]
 is_a: MS:1000693 ! Thermo Finnigan software
 is_a: MS:1001455 ! acquisition software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000534
 name: MassLynx
 def: "Micromass software for data acquisition and analysis." [PSI:MS]

 is_a: MS:1000694 ! Waters software

 is_a: MS:1001455 ! acquisition software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000535
 name: FlexAnalysis
 def: "Bruker software for data analysis." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001455 ! acquisition software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001455 ! acquisition software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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]

 synonym: "wolf" EXACT []
 is_a: MS:1001457 ! data processing software
 
 [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
 is_a: MS:1001455 ! acquisition software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000540
 name: FlexControl
 def: "Bruker software for data acquisition." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001455 ! acquisition 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:1001457 ! data processing 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:1001457 ! data processing 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 mzML 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:1001458 ! spectrum generation information
 
 [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: "OBSOLETE Time Unit." [PSI:MS]

 comment: This term was made obsolete because it was redundant with the Unit Ontology term time unit (UO:0000003).

 is_obsolete: true
 
 [Term]
 id: MS:1000551
 name: Analyst

 def: "SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition." [PSI:MS]
 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001455 ! acquisition software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000552
 name: maldi spot identifier

 def: "OBSOLETE Maldi Spot Identifier." [PSI:MS]
 comment: This former purgatory term was made obsolete.
 is_obsolete: true

 
 [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:1001457 ! data processing 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: mass spectrometer file format
 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]
 is_a: MS:1001459 ! file format
 
 [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 ! source data file

 
 [Term]
 id: MS:1000562

 name: ABI WIFF format

 def: "Applied Biosystems WIFF file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000563

 name: Thermo RAW format

 def: "Thermo Scientific RAW file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000564

 name: PSI mzData format

 def: "Proteomics Standards Inititative mzData file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000565

 name: Micromass PKL format

 def: "Micromass PKL file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000566

 name: ISB mzXML format

 def: "Institute of Systems Biology mzXML file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000567

 name: Bruker/Agilent YEP format

 def: "Bruker/Agilent YEP file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [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]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000561 ! data file checksum type
 
 [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]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000561 ! data file checksum type
 
 [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: source data file
 def: "Data file from which an entity is sourced." [PSI:MS]

 synonym: "source file" EXACT []
 relationship: part_of MS:1001458 ! spectrum generation information

 is_a: MS:1000499 ! spectrum attribute

 
 [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: "Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment." [PSI:MS]
 synonym: "full spectrum" EXACT []
 synonym: "Q1 spectrum" EXACT []
 synonym: "Q3 spectrum" EXACT []
 synonym: "Single-Stage Mass Spectrometry" EXACT []
 is_a: MS:1000294 ! mass spectrum
 
 [Term]
 id: MS:1000580
 name: MSn spectrum

 def: "MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n." [PSI:MS]

 synonym: "multiple-stage mass spectrometry spectrum" EXACT []
 synonym: "nth generation product ion spectrum" EXACT []
 synonym: "product ion spectrum" EXACT []
 is_a: MS:1000294 ! mass spectrum
 
 [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:1000294 ! mass spectrum
 
 [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]
 synonym: "MIM spectrum" EXACT []
 synonym: "multiple ion monitoring spectrum" EXACT []
 synonym: "selected ion monitoring spectrum" EXACT []
 is_a: MS:1000294 ! mass spectrum
 
 [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]

 synonym: "MRM spectrum" EXACT []
 synonym: "multiple reaction monitoring spectrum" EXACT []
 synonym: "selected reaction monitoring spectrum" EXACT []
 is_a: MS:1000294 ! mass spectrum
 
 [Term]
 id: MS:1000584

 name: mzML format

 def: "Proteomics Standards Inititative mzML file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000585

 name: contact attribute
 def: "Details about a person or organization to contact in case of concern or discussion about the file." [PSI:MS]

 is_a: MS:1000547 ! object attribute
 relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
 
 [Term]
 id: MS:1000586
 name: contact name

 def: "Name of the contact person or organization." [PSI:MS]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1000585 ! contact attribute

 
 [Term]
 id: MS:1000587
 name: contact address

 def: "Postal address of the contact person or organization." [PSI:MS]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1000585 ! contact attribute

 
 [Term]
 id: MS:1000588
 name: contact URL

 def: "Uniform Resource Locator related to the contact person or organization." [PSI:MS]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1000585 ! contact attribute

 
 [Term]
 id: MS:1000589
 name: contact email

 def: "Email address of the contact person or organization." [PSI:MS]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1000585 ! contact attribute

 
 [Term]
 id: MS:1000590

 name: contact affiliation

 def: "Home institution of the contact person." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1000585 ! contact attribute

 
 [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:1001457 ! data processing 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:1001486 ! data filtering
 
 [Term]
 id: MS:1000595
 name: time array
 def: "A data array of relative time offset values from a reference time." [PSI:MS]

 xref: binary-data-type:MS\:1000521 "32-bit float"
 xref: binary-data-type:MS\:1000523 "64-bit float"

 is_a: MS:1000513 ! binary data array
 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute
 
 [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:1001458 ! spectrum generation information
 
 [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
 
 [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
 
 [Term]
 id: MS:1000600
 name: Proteios

 def: "Database application and analysis platform for proteomics." [PSI:MS, source:http://www.proteios.org]

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000601
 name: ProteinLynx Global Server
 def: "Waters software for data analysis." [PSI:MS]
 is_a: MS:1000694 ! Waters software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000602

 name: Shimadzu MALDI-TOF instrument model
 def: "Shimadzu MALDI-TOF 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 MALDI-TOF instrument model

 
 [Term]
 id: MS:1000608
 name: AXIMA-QIT
 def: "Shimadzu Biotech AXIMA-QIT MS." [PSI:MS]

 is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model

 
 [Term]
 id: MS:1000609
 name: AXIMA-CFR plus
 def: "Shimadzu Biotech AXIMA-CFR plus MS." [PSI:MS]

 is_a: MS:1000602 ! Shimadzu MALDI-TOF 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 MALDI-TOF 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 MALDI-TOF 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 MALDI-TOF instrument model

 
 [Term]
 id: MS:1000613

 name: DTA format
 def: "SEQUEST DTA file format." [PSI:MS]

 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000614

 name: ProteinLynx Global Server mass spectrum XML format

 def: "Peak list file format used by ProteinLynx Global Server." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000615

 name: ProteoWizard software
 def: "ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb." [PSI:MS]

 synonym: "pwiz" EXACT []
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000503 ! scan attribute
 
 [Term]
 id: MS:1000617
 name: wavelength array
 def: "A data array of electromagnetic radiation wavelength values." [PSI:MS]

 xref: binary-data-type:MS\:1000521 "32-bit float"
 xref: binary-data-type:MS\:1000523 "64-bit float"

 is_a: MS:1000513 ! binary data array
 relationship: has_units UO:0000018 ! nanometer
 
 [Term]
 id: MS:1000618
 name: highest observed wavelength
 def: "Highest wavelength observed in an EMR spectrum." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 is_a: MS:1003058 ! spectrum property

 is_a: MS:1000808 ! chromatogram attribute
 relationship: has_units UO:0000018 ! nanometer
 
 [Term]
 id: MS:1000619
 name: lowest observed wavelength
 def: "Lowest wavelength observed in an EMR spectrum." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 is_a: MS:1003058 ! spectrum property

 is_a: MS:1000808 ! chromatogram attribute
 relationship: has_units UO:0000018 ! nanometer
 
 [Term]
 id: MS:1000620
 name: PDA spectrum
 def: "OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum)." [PSI:MS]

 comment: This term was made obsolete because it was replaced by absorption spectrum (MS:1000806).

 is_a: MS:1000524 ! data file content
 is_a: MS:1000559 ! spectrum type
 is_obsolete: true
 
 [Term]
 id: MS:1000621
 name: photodiode array detector

 def: "An array detector used to record spectra in the ultraviolet and visible region of light." [PSI:MS]

 synonym: "PDA" EXACT []

 is_a: MS:1000345 ! array detector

 
 [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: "Representation of a chromatographic separation attribute measurement versus time." [PSI:MS]

 relationship: part_of MS:1001458 ! spectrum generation information
 
 [Term]
 id: MS:1000626
 name: chromatogram type

 def: "Type of chromatogram measurement being represented." [PSI:MS]

 relationship: part_of MS:1000625 ! chromatogram
 
 [Term]
 id: MS:1000627
 name: selected ion current chromatogram

 def: "Representation of an array of the measurements of a specific single ion current versus time." [PSI:MS]

 synonym: "SIC chromatogram" EXACT []

 is_a: MS:1000810 ! ion current chromatogram

 
 [Term]
 id: MS:1000628
 name: basepeak chromatogram

 def: "Representation of an array of the most intense peaks versus time." [PSI:MS]
 is_a: MS:1000810 ! ion current chromatogram

 
 [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:1000131 ! number of detector counts

 relationship: has_units MS:1000132 ! percent of base peak
 relationship: has_units MS:1000814 ! counts per second
 relationship: has_units MS:1000905 ! percent of base peak times 100
 relationship: has_units UO:0000269 ! absorbance 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]
 relationship: part_of MS:1001458 ! spectrum generation information
 
 [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:1000131 ! number of detector counts

 relationship: has_units MS:1000132 ! percent of base peak
 relationship: has_units MS:1000814 ! counts per second
 relationship: has_units MS:1000905 ! percent of base peak times 100
 relationship: has_units UO:0000269 ! absorbance unit
 
 [Term]
 id: MS:1000632
 name: Q-Tof Premier

 def: "Waters oa-ToF based Q-Tof Premier." [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: Proteome Discoverer
 def: "Thermo Scientific software for data analysis of peptides and proteins." [PSI:MS]
 is_a: MS:1000693 ! Thermo Finnigan software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000651
 name: 3200 QTRAP

 def: "SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200." [PSI:MS]
 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000652

 name: 4800 Plus MALDI TOF/TOF

 def: "SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer." [PSI:MS]
 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000653
 name: API 3200

 def: "SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS." [PSI:MS]
 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000654
 name: API 5000

 def: "SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS." [PSI:MS]
 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000655
 name: QSTAR Elite

 def: "SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite." [PSI:MS]
 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000656
 name: QSTAR Pulsar

 def: "Applied Biosystems|MDS SCIEX QSTAR Pulsar." [PSI:MS]

 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000657
 name: QSTAR XL

 def: "Applied Biosystems|MDS SCIEX QSTAR XL." [PSI:MS]

 is_a: MS:1000121 ! 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: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS]
 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001455 ! acquisition software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000661
 name: GPS Explorer

 def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS]
 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001455 ! acquisition software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000662
 name: LightSight Software

 def: "SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification." [PSI:MS]
 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000663
 name: ProteinPilot Software

 def: "SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant." [PSI:MS]
 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000664
 name: TissueView Software
 def: "Applied Biosystems|MDS SCIEX software for tissue imaging." [PSI:MS]

 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000666
 name: MRMPilot Software
 def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS]

 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000667
 name: BioAnalyst
 def: "Applied Biosystems|MDS SCIEX software for bio-related data exploration." [PSI:MS]

 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000668
 name: Pro ID
 def: "Applied Biosystems|MDS SCIEX software for protein identification." [PSI:MS]

 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000671
 name: Pro BLAST
 def: "Applied Biosystems|MDS SCIEX software for MS-BLAST identification." [PSI:MS]

 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000672

 name: Cliquid

 def: "SCIEX Cliquid software for data analysis and quantitation." [PSI:MS]
 is_a: MS:1000690 ! 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 ! SCIEX software

 
 [Term]
 id: MS:1000674
 name: MultiQuant
 def: "Applied Biosystems|MDS SCIEX software for MRM-based quantitation." [PSI:MS]

 is_a: MS:1000690 ! SCIEX software

 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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: 6520A Quadrupole Time-of-Flight LC/MS
 def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [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
 is_a: MS:1001455 ! acquisition software
 
 [Term]
 id: MS:1000679
 name: MassHunter Easy Access
 def: "Software for open access data acquisition." [PSI:MS]
 is_a: MS:1000689 ! Agilent software
 is_a: MS:1001455 ! acquisition 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000681
 name: MassHunter Quantitative Analysis

 def: "Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data." [PSI:MS]

 is_a: MS:1000689 ! Agilent software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000682
 name: MassHunter Metabolite ID
 def: "Software for identification of metabolites." [PSI:MS]
 is_a: MS:1000689 ! Agilent software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000683
 name: MassHunter BioConfirm
 def: "Software for protein characterization." [PSI:MS]
 is_a: MS:1000689 ! Agilent software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001455 ! acquisition software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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: SCIEX software
 def: "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: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS]
 is_a: MS:1001556 ! Bruker Daltonics apex series
 
 [Term]
 id: MS:1000696
 name: autoflex III smartbeam
 def: "Bruker Daltonics' autoflex III smartbeam: MALDI TOF." [PSI:MS]
 is_a: MS:1001534 ! Bruker Daltonics flex series
 
 [Term]
 id: MS:1000697
 name: Bruker Daltonics 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: ESI TOF, Nanospray, APCI, APPI." [PSI:MS]

 is_a: MS:1000697 ! Bruker Daltonics HCT Series

 
 [Term]
 id: MS:1000699
 name: HCTultra PTM

 def: "Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR." [PSI:MS]
 is_a: MS:1000697 ! Bruker Daltonics HCT Series

 
 [Term]
 id: MS:1000700
 name: HCTultra ETD II

 def: "Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD." [PSI:MS]
 is_a: MS:1000697 ! Bruker Daltonics HCT Series

 
 [Term]
 id: MS:1000701
 name: microflex LT
 def: "Bruker Daltonics' microflex LT: MALDI TOF." [PSI:MS]
 is_a: MS:1001534 ! Bruker Daltonics flex series
 
 [Term]
 id: MS:1000702
 name: micrOTOF
 def: "Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI." [PSI:MS]
 is_a: MS:1001536 ! Bruker Daltonics micrOTOF series
 
 [Term]
 id: MS:1000703
 name: micrOTOF-Q
 def: "Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS]
 is_a: MS:1001536 ! Bruker Daltonics micrOTOF series
 
 [Term]
 id: MS:1000704
 name: micrOTOF-Q II
 def: "Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS]
 is_a: MS:1001536 ! Bruker Daltonics micrOTOF series
 
 [Term]
 id: MS:1000705
 name: ultraflex III TOF/TOF

 def: "Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF." [PSI:MS]

 is_a: MS:1001534 ! Bruker Daltonics flex series
 
 [Term]
 id: MS:1000706
 name: apexControl
 def: "Bruker software for data acquisition." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001455 ! acquisition software
 
 [Term]
 id: MS:1000707
 name: BioTools
 def: "Bruker software for data analysis." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000708
 name: CLINPROT
 def: "Bruker CLINPROT software." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000709
 name: CLINPROT micro
 def: "Bruker CLINPROT micro software." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000714
 name: Compass for micrOTOF
 def: "Bruker Compass for micrOTOF software." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000715
 name: Compass OpenAccess
 def: "Bruker compass OpenAccess software." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000718
 name: CompassXtract
 def: "Bruker software library for data access." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000719
 name: DataAnalysis
 def: "Bruker software for data analysis." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000720
 name: dpControl
 def: "Bruker software for data acquisition." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001455 ! acquisition software
 
 [Term]
 id: MS:1000721
 name: esquireControl
 def: "Bruker software for data acquisition." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001455 ! acquisition software
 
 [Term]
 id: MS:1000722
 name: flexImaging
 def: "Bruker software for data analysis." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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
 is_a: MS:1001455 ! acquisition software
 
 [Term]
 id: MS:1000726
 name: micrOTOFcontrol
 def: "Bruker software for data acquisition." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001455 ! acquisition 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000729
 name: PROTEINEER
 def: "Bruker PROTEINEER software." [PSI:PI]
 is_a: MS:1000692 ! Bruker software
 
 [Term]
 id: MS:1000730
 name: PROTEINEER dp
 def: "Bruker PROTEINEER dp software." [PSI:PI]
 is_a: MS:1000692 ! Bruker software
 
 [Term]
 id: MS:1000731
 name: PROTEINEER fc
 def: "Bruker PROTEINEER fc software." [PSI:PI]
 is_a: MS:1000692 ! Bruker software
 
 [Term]
 id: MS:1000732
 name: PROTEINEER spII
 def: "Bruker PROTEINEER spII software." [PSI:PI]
 is_a: MS:1000692 ! Bruker software
 
 [Term]
 id: MS:1000733
 name: PROTEINEER-LC
 def: "Bruker PROTEINEER-LC software." [PSI:PI]
 is_a: MS:1000692 ! Bruker software
 
 [Term]
 id: MS:1000734
 name: ProteinScape
 def: "Bruker ProteinScape software." [PSI:PI]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001456 ! analysis 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
 is_a: MS:1001456 ! analysis software
 is_a: MS:1001457 ! data processing software
 
 [Term]
 id: MS:1000737
 name: spControl
 def: "Bruker software for data acquisition." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 is_a: MS:1001455 ! acquisition 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

 is_a: MS:1001139 ! quantitation software name

 
 [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 ! mass spectrometer file format
 
 [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 format

 def: "Thermo Finnigan SRF file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 is_a: MS:1001040 ! intermediate analysis format
 
 [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 ion m/z

 def: "Mass-to-charge ratio of an selected ion." [PSI:MS]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000455 ! ion selection attribute
 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:1001486 ! data filtering
 
 [Term]
 id: MS:1000747
 name: completion time
 def: "The time that a data processing action was finished." [PSI:MS]

 xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."

 is_a: MS:1000630 ! data processing parameter
 
 [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:1001456 ! analysis software
 is_a: MS:1001457 ! data processing 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: "OBSOLETE Corrects retention time distortions between maps." [PSI:MS]
 comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch.

 is_a: MS:1000752 ! TOPP software

 is_obsolete: true

 
 [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: "OBSOLETE Removes noise from profile spectra by using different smoothing techniques." [PSI:MS]
 comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch.

 is_a: MS:1000752 ! TOPP software

 is_obsolete: true

 
 [Term]
 id: MS:1000763
 name: PeakPicker

 def: "OBSOLETE Finds mass spectrometric peaks in profile mass spectra." [PSI:MS]
 comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch.

 is_a: MS:1000752 ! TOPP software

 is_obsolete: true

 
 [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: "OBSOLETE Applies a filter to peak spectra." [PSI:MS]
 comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch.

 is_a: MS:1000752 ! TOPP software

 is_obsolete: true

 
 [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 ! source data file

 
 [Term]
 id: MS:1000768
 name: Thermo nativeID format

 def: "Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger." [PSI:MS]

 is_a: MS:1000767 ! native spectrum identifier format
 
 [Term]
 id: MS:1000769
 name: Waters nativeID format

 def: "Native format defined by 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: "Native format defined by 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: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS]

 is_a: MS:1000767 ! native spectrum identifier format
 
 [Term]
 id: MS:1000772
 name: Bruker BAF nativeID format

 def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS]

 is_a: MS:1000767 ! native spectrum identifier format
 
 [Term]
 id: MS:1000773
 name: Bruker FID nativeID format

 def: "Native format defined by 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: "Native format defined by 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: "Native format defined by 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: "Native format defined by 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: "Native format defined by 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 ambiguously 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 modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible." [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: "binomial smoothing" EXACT []
 synonym: "Weierstrass transform" 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]

 xref: binary-data-type:MS\:1000519 "32-bit integer"
 xref: binary-data-type:MS\:1000521 "32-bit float"
 xref: binary-data-type:MS\:1000522 "64-bit integer"
 xref: binary-data-type:MS\:1000523 "64-bit float"
 xref: binary-data-type:MS\:1001479 "null-terminated ASCII string"

 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000513 ! binary data array
 
 [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:1000131 ! number of detector counts

 relationship: has_units MS:1000132 ! percent of base peak
 relationship: has_units MS:1000814 ! counts per second
 relationship: has_units MS:1000905 ! percent of base peak times 100
 relationship: has_units UO:0000269 ! absorbance 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:1000131 ! number of detector counts

 relationship: has_units MS:1000132 ! percent of base peak
 relationship: has_units MS:1000814 ! counts per second
 relationship: has_units MS:1000905 ! percent of base peak times 100
 relationship: has_units UO:0000269 ! absorbance 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:1000579 ! MS1 spectrum
 
 [Term]
 id: MS:1000790
 name: time-delayed fragmentation spectrum

 def: "MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation." [PSI:MS]

 is_a: MS:1000580 ! MSn spectrum
 
 [Term]
 id: MS:1000791
 name: enhanced resolution scan
 def: "OBSOLETE Scan with enhanced resolution." [PSI:MS]

 comment: This term was made obsolete because it was merged with zoom scan (MS:1000497).

 is_obsolete: true
 
 [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 window upper limit
 def: "OBSOLETE The highest m/z being isolated in an isolation window." [PSI:MS]

 comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829.

 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
 is_obsolete: true
 
 [Term]
 id: MS:1000794
 name: isolation window lower limit
 def: "OBSOLETE The lowest m/z being isolated in an isolation window." [PSI:MS]

 comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829.

 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
 is_obsolete: true
 
 [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: "Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file." [PSI:MS]

 comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list.
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1001405 ! spectrum identification result details

 is_a: MS:1000499 ! spectrum attribute

 
 [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.
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1001405 ! spectrum identification result details

 is_a: MS:1003058 ! spectrum property

 
 [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.
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1001405 ! spectrum identification result details

 is_a: MS:1003058 ! spectrum property

 
 [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]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000531 ! software
 
 [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
 
 [Term]
 id: MS:1000803
 name: analyzer scan offset
 def: "Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000503 ! scan attribute
 relationship: has_units MS:1000040 ! m/z
 
 [Term]
 id: MS:1000804
 name: electromagnetic radiation spectrum
 def: "A plot of the relative intensity of electromagnetic radiation as a function of the wavelength." [PSI:MS]
 synonym: "EMR spectrum" EXACT []
 is_a: MS:1000524 ! data file content
 is_a: MS:1000559 ! spectrum type
 
 [Term]
 id: MS:1000805
 name: emission spectrum
 def: "A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited." [PSI:MS]
 is_a: MS:1000524 ! data file content
 is_a: MS:1000559 ! spectrum type
 
 [Term]
 id: MS:1000806
 name: absorption spectrum
 def: "A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited." [PSI:MS]
 is_a: MS:1000524 ! data file content
 is_a: MS:1000559 ! spectrum type
 
 [Term]
 id: MS:1000807
 name: Th/s
 def: "Unit describing the scan rate of a spectrum in Thomson per second." [PSI:MS]

 is_a: UO:0000000 ! unit

 
 [Term]
 id: MS:1000808
 name: chromatogram attribute
 def: "Chromatogram properties that are associated with a value." [PSI:MS]
 is_a: MS:1000547 ! object attribute
 relationship: part_of MS:1000625 ! chromatogram
 
 [Term]
 id: MS:1000809
 name: chromatogram title
 def: "A free-form text title describing a chromatogram." [PSI:MS]
 comment: This is the preferred storage place for the spectrum title.
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000808 ! chromatogram attribute
 
 [Term]
 id: MS:1000810

 name: ion current chromatogram
 def: "Representation of the current of ions versus time." [PSI:MS]

 is_a: MS:1000524 ! data file content
 is_a: MS:1000626 ! chromatogram type
 
 [Term]
 id: MS:1000811
 name: electromagnetic radiation chromatogram

 def: "Representation of electromagnetic properties versus time." [PSI:MS]

 synonym: "EMR radiation chromatogram" EXACT []
 is_a: MS:1000524 ! data file content
 is_a: MS:1000626 ! chromatogram type
 
 [Term]
 id: MS:1000812
 name: absorption chromatogram

 def: "Representation of light absorbed by the sample versus time." [PSI:MS]

 is_a: MS:1000811 ! electromagnetic radiation chromatogram
 
 [Term]
 id: MS:1000813
 name: emission chromatogram

 def: "Representation of light emitted by the sample versus time." [PSI:MS]

 is_a: MS:1000811 ! electromagnetic radiation chromatogram
 
 [Term]
 id: MS:1000814
 name: counts per second
 def: "The number of counted events observed per second in one or a group of elements of a detector." [PSI:MS]
 is_a: MS:1000043 ! intensity unit
 
 [Term]
 id: MS:1000815

 name: Bruker BAF format

 def: "Bruker BAF raw file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000816

 name: Bruker U2 format

 def: "Bruker HyStar U2 file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000817
 name: HyStar
 def: "Bruker software for hyphenated experiments." [PSI:MS]
 is_a: MS:1000692 ! Bruker software
 
 [Term]
 id: MS:1000818
 name: Acquity UPLC PDA
 def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
 is_a: MS:1000126 ! Waters instrument model

 is_a: MS:1000621 ! photodiode array detector

 
 [Term]
 id: MS:1000819
 name: Acquity UPLC FLR
 def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
 is_a: MS:1000126 ! Waters instrument model

 is_a: MS:1002308 ! fluorescence detector

 
 [Term]
 id: MS:1000820
 name: flow rate array
 def: "A data array of flow rate measurements." [PSI:MS]

 xref: binary-data-type:MS\:1000521 "32-bit float"
 xref: binary-data-type:MS\:1000523 "64-bit float"

 is_a: MS:1000513 ! binary data array

 relationship: has_units UO:0000271 ! microliters per minute

 
 [Term]
 id: MS:1000821
 name: pressure array
 def: "A data array of pressure measurements." [PSI:MS]

 xref: binary-data-type:MS\:1000521 "32-bit float"
 xref: binary-data-type:MS\:1000523 "64-bit float"

 is_a: MS:1000513 ! binary data array
 relationship: has_units UO:0000110 ! pascal
 
 [Term]
 id: MS:1000822
 name: temperature array
 def: "A data array of temperature measurements." [PSI:MS]

 xref: binary-data-type:MS\:1000521 "32-bit float"
 xref: binary-data-type:MS\:1000523 "64-bit float"

 is_a: MS:1000513 ! binary data array
 relationship: has_units UO:0000012 ! kelvin
 
 [Term]
 id: MS:1000823
 name: Bruker U2 nativeID format

 def: "Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS]

 is_a: MS:1000767 ! native spectrum identifier format
 
 [Term]
 id: MS:1000824
 name: no nativeID format
 def: "No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format." [PSI:MS]
 is_a: MS:1000767 ! native spectrum identifier format
 
 [Term]
 id: MS:1000825

 name: Bruker FID format

 def: "Bruker FID file format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000826
 name: elution time

 def: "The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography." [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:0000010 ! second
 relationship: has_units UO:0000031 ! minute
 
 [Term]
 id: MS:1000827
 name: isolation window target m/z
 def: "The primary or reference m/z about which the isolation window is defined." [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:1000828
 name: isolation window lower offset

 def: "The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [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:1000829
 name: isolation window upper offset

 def: "The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [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:1000831
 name: sample preparation
 def: "Properties of the preparation steps which took place before the measurement was performed." [PSI:MS]
 is_a: MS:1000547 ! object attribute

 relationship: part_of MS:1000548 ! sample attribute

 
 [Term]
 id: MS:1000832
 name: MALDI matrix application
 def: "Attributes to describe the technique how the sample is prepared with the matrix solution." [PSI:MS]

 relationship: part_of MS:1000831 ! sample preparation

 
 [Term]
 id: MS:1000833
 name: matrix application type
 def: "Describes the technique how the matrix is put on the sample target." [PSI:MS]
 relationship: part_of MS:1000832 ! MALDI matrix application
 
 [Term]
 id: MS:1000834
 name: matrix solution
 def: "Describes the chemical solution used as matrix." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000832 ! MALDI matrix application
 
 [Term]
 id: MS:1000835
 name: matrix solution concentration
 def: "Concentration of the chemical solution used as matrix." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000832 ! MALDI matrix application

 relationship: has_units UO:0000175 ! gram per liter

 
 [Term]
 id: MS:1000836

 name: dried droplet MALDI matrix preparation
 def: "Dried droplet in MALDI matrix preparation." [PSI:MS]

 is_a: MS:1000833 ! matrix application type
 
 [Term]
 id: MS:1000837

 name: printed MALDI matrix preparation
 def: "Printed MALDI matrix preparation." [PSI:MS]

 is_a: MS:1000833 ! matrix application type
 
 [Term]
 id: MS:1000838

 name: sprayed MALDI matrix preparation
 def: "Sprayed MALDI matrix preparation." [PSI:MS]

 is_a: MS:1000833 ! matrix application type
 
 [Term]
 id: MS:1000839

 name: precoated MALDI sample plate
 def: "Precoated MALDI sample plate." [PSI:MS]

 is_a: MS:1000833 ! matrix application type

 is_a: MS:1001938 ! sample plate type

 
 [Term]
 id: MS:1000840
 name: laser
 def: "Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation." [PSI:MS]
 relationship: part_of MS:1000482 ! source attribute
 
 [Term]
 id: MS:1000841
 name: laser attribute
 def: "Laser properties that are associated with a value." [PSI:MS]
 relationship: part_of MS:1000840 ! laser
 
 [Term]
 id: MS:1000842
 name: laser type

 def: "Type of laser used for desorption purpose." [PSI:MS]

 relationship: part_of MS:1000840 ! laser
 
 [Term]
 id: MS:1000843
 name: wavelength

 def: "OBSOLETE The distance between two peaks of the emitted laser beam." [PSI:MS]
 comment: This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242).

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000841 ! laser attribute
 relationship: has_units UO:0000018 ! nanometer

 is_obsolete: true

 
 [Term]
 id: MS:1000844
 name: focus diameter x
 def: "Describes the diameter of the laser beam in x direction." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000841 ! laser attribute
 relationship: has_units UO:0000017 ! micrometer
 
 [Term]
 id: MS:1000845
 name: focus diameter y
 def: "Describes the diameter of the laser beam in y direction." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000841 ! laser attribute
 relationship: has_units UO:0000017 ! micrometer
 
 [Term]
 id: MS:1000846
 name: pulse energy
 def: "Describes output energy of the laser system. May be attenuated by filters or other means." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000841 ! laser attribute
 relationship: has_units UO:0000112 ! joule
 
 [Term]
 id: MS:1000847
 name: pulse duration
 def: "Describes how long the laser beam was emitted from the laser device." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000841 ! laser attribute
 relationship: has_units UO:0000150 ! nanosecond
 
 [Term]
 id: MS:1000848
 name: attenuation
 def: "Describes the reduction of the intensity of the laser beam energy." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000841 ! laser attribute
 relationship: has_units UO:0000187 ! percent
 
 [Term]
 id: MS:1000849
 name: impact angle
 def: "Describes the angle between the laser beam and the sample target." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000841 ! laser attribute
 relationship: has_units UO:0000185 ! degree
 
 [Term]
 id: MS:1000850
 name: gas laser
 def: "Laser which is powered by a gaseous medium." [PSI:MS]
 is_a: MS:1000842 ! laser type
 
 [Term]
 id: MS:1000851
 name: solid-state laser
 def: "Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states." [PSI:MS]
 is_a: MS:1000842 ! laser type
 
 [Term]
 id: MS:1000852
 name: dye-laser
 def: "Dye lasers use an organic dye as the gain medium." [PSI:MS]
 is_a: MS:1000842 ! laser type
 
 [Term]
 id: MS:1000853
 name: free electron laser
 def: "Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term." [PSI:MS]
 is_a: MS:1000842 ! laser type
 
 [Term]
 id: MS:1000854
 name: LTQ XL
 def: "Thermo Scientific LTQ XL MS." [PSI:MS]
 is_a: MS:1000494 ! Thermo Scientific instrument model
 
 [Term]
 id: MS:1000855
 name: LTQ Velos
 def: "Thermo Scientific LTQ Velos MS." [PSI:MS]
 is_a: MS:1000494 ! Thermo Scientific instrument model
 
 [Term]
 id: MS:1000856
 name: LTQ Velos ETD
 def: "Thermo Scientific LTQ Velos MS with ETD." [PSI:MS]
 is_a: MS:1000494 ! Thermo Scientific instrument model
 
 [Term]
 id: MS:1000857
 name: run attribute
 def: "Properties of the described run." [PSI:MS]

 is_a: MS:1000547 ! object attribute

 
 [Term]
 id: MS:1000858
 name: fraction identifier

 def: "Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information." [PSI:MS]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000857 ! run attribute
 
 [Term]
 id: MS:1000859
 name: molecule

 def: "Group of two or more atoms held together by chemical bonds." [https://en.wikipedia.org/wiki/Molecule]
 is_a: MS:1000881 ! molecular entity

 
 [Term]
 id: MS:1000860
 name: peptide

 def: "A molecule of low molecular weight that is composed of two or more amino acid residues." [PSI:MS]
 is_a: MS:1000859 ! molecule

 
 [Term]
 id: MS:1000861

 name: molecular entity property
 def: "A physical characteristic of a molecular entity." [PSI:MS]
 relationship: part_of MS:1000881 ! molecular entity

 
 [Term]
 id: MS:1000862
 name: isoelectric point
 def: "The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS]

 synonym: "pI" EXACT []

 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 is_a: MS:1000861 ! molecular entity property

 
 [Term]
 id: MS:1000863
 name: predicted isoelectric point
 def: "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm." [PSI:MS]

 synonym: "predicted pI" EXACT []

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000862 ! isoelectric point
 
 [Term]
 id: MS:1000864

 name: chemical formula
 def: "A combination of symbols used to express the chemical composition of a molecule." [EDAM:0846]
 is_a: MS:1003033 ! molecular entity attribute

 
 [Term]
 id: MS:1000865
 name: empirical formula
 def: "A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1000864 ! chemical formula

 
 [Term]
 id: MS:1000866
 name: molecular formula
 def: "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1000864 ! chemical formula

 
 [Term]
 id: MS:1000867
 name: structural formula
 def: "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1000864 ! chemical formula

 
 [Term]
 id: MS:1000868

 name: SMILES formula
 def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1000864 ! chemical formula

 
 [Term]
 id: MS:1000869
 name: collision gas pressure
 def: "The gas pressure of the collision gas used for collisional excitation." [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:0000110 ! pascal
 
 [Term]
 id: MS:1000870
 name: 4000 QTRAP

 def: "OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000." [PSI:MS]

 comment: This term was obsoleted because was redundant to MS:1000139.

 is_a: MS:1000121 ! SCIEX instrument model

 is_obsolete: true

 
 [Term]
 id: MS:1000871
 name: SRM software
 def: "Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs." [PSI:MS]
 is_a: MS:1000531 ! software
 
 [Term]
 id: MS:1000872
 name: MaRiMba

 def: "Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba]

 is_a: MS:1000871 ! SRM software
 
 [Term]
 id: MS:1000873
 name: peptide attribute calculation software

 def: "Software used to predict or calculate numerical attributes of peptides." [PSI:MS]

 is_a: MS:1000531 ! software
 
 [Term]
 id: MS:1000874
 name: SSRCalc

 def: "Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence." [http://hs2.proteome.ca/SSRCalc/SSRCalc.html]

 is_a: MS:1000873 ! peptide attribute calculation software
 
 [Term]
 id: MS:1000875
 name: declustering potential
 def: "Potential difference between the orifice and the skimmer 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:0000218 ! volt
 
 [Term]
 id: MS:1000876
 name: cone voltage

 def: "Potential difference between the sampling cone/orifice 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:0000218 ! volt
 
 [Term]
 id: MS:1000877

 name: tube lens voltage
 def: "Potential difference setting of the tube lens 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:0000218 ! volt
 
 [Term]
 id: MS:1000878
 name: external reference identifier
 def: "An identifier/accession number to an external reference database." [PSI:MS]

 is_a: MS:1002840 ! external reference data

 
 [Term]
 id: MS:1000879
 name: PubMed identifier
 def: "A unique identifier for a publication in the PubMed database (MIR:00000015)." [PSI:MS]
 xref: value-type:xsd\:integer "The allowed value-type for this CV term."
 is_a: MS:1000878 ! external reference identifier
 
 [Term]
 id: MS:1000880
 name: interchannel delay
 def: "The duration of intervals between scanning, during which the instrument configuration is switched." [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:0000010 ! second
 
 [Term]
 id: MS:1000881

 name: molecular entity
 def: "Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [https://en.wikipedia.org/wiki/Molecular_entity]

 relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
 
 [Term]
 id: MS:1000882
 name: protein

 def: "A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene." [PSI:MS]
 is_a: MS:1000859 ! molecule

 
 [Term]
 id: MS:1000883
 name: protein short name
 def: "A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN)." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000884 ! protein attribute
 
 [Term]
 id: MS:1000884
 name: protein attribute

 def: "An nonphysical characterstic attributed to a specific protein." [PSI:MS]

 relationship: part_of MS:1000882 ! protein

 is_a: MS:1001806 ! quantification object attribute

 
 [Term]
 id: MS:1000885
 name: protein accession

 def: "Identifier for a specific protein in a database." [PSI:MS]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000884 ! protein attribute

 is_a: MS:1003046 ! peptide-to-protein mapping attribute

 
 [Term]
 id: MS:1000886
 name: protein name
 def: "A long name describing the function of the protein." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000884 ! protein attribute
 
 [Term]
 id: MS:1000887
 name: peptide attribute

 def: "Nonphysical characteristic attributed to a peptide." [PSI:MS]

 relationship: part_of MS:1000860 ! peptide
 
 [Term]
 id: MS:1000888

 name: stripped peptide sequence
 def: "Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away." [PSI:MS]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1003050 ! peptidoform attribute

 
 [Term]
 id: MS:1000889

 name: peptidoform sequence
 def: "Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present." [PSI:MS]

 comment: Make it more general as there are actually many other ways to display a modified peptide sequence.

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1003050 ! peptidoform attribute

 
 [Term]
 id: MS:1000890

 name: peptidoform labeling state

 def: "A state description of how a peptide might be isotopically or isobarically labelled." [PSI:MS]

 is_a: MS:1003050 ! peptidoform attribute

 
 [Term]
 id: MS:1000891

 name: heavy labeled peptidoform

 def: "A peptide that has been created or labelled with some heavier-than-usual isotopes." [PSI:MS]

 is_a: MS:1000890 ! peptidoform labeling state

 
 [Term]
 id: MS:1000892

 name: unlabeled peptidoform

 def: "A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:MS]

 synonym: "light labeled peptide" EXACT []

 is_a: MS:1000890 ! peptidoform labeling state

 
 [Term]
 id: MS:1000893

 name: peptidoform group label

 def: "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1003050 ! peptidoform attribute

 
 [Term]
 id: MS:1000894
 name: retention time

 def: "A time interval from the start of chromatography when an analyte exits a chromatographic column." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."

 is_a: MS:1003050 ! peptidoform attribute

 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute

 
 [Term]
 id: MS:1000895
 name: local retention time

 def: "A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup." [PSI:MS]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000894 ! retention time
 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute
 
 [Term]
 id: MS:1000896
 name: normalized retention time

 def: "A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup." [PSI:MS]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000894 ! retention time
 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute
 
 [Term]
 id: MS:1000897
 name: predicted retention time

 def: "A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application." [PSI:MS]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000894 ! retention time
 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute
 
 [Term]
 id: MS:1000898
 name: standard
 def: "Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence." [PSI:MS]
 relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
 
 [Term]
 id: MS:1000899
 name: de facto standard
 def: "A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard." [PSI:MS]
 is_a: MS:1000898 ! standard
 
 [Term]
 id: MS:1000900
 name: minimum information standard
 def: "A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result." [PSI:MS]
 is_a: MS:1000898 ! standard
 
 [Term]
 id: MS:1000901
 name: retention time normalization standard
 def: "A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column." [PSI:MS]
 is_a: MS:1000898 ! standard
 
 [Term]
 id: MS:1000902
 name: H-PINS retention time normalization standard

 def: "The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column." [DOI:10.1074/mcp.M800569-MCP200, PMID:19411281]

 is_a: MS:1000901 ! retention time normalization standard
 
 [Term]
 id: MS:1000903
 name: product ion series ordinal
 def: "The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion)." [PSI:PI]
 xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."

 is_a: MS:1001221 ! product ion attribute

 
 [Term]
 id: MS:1000904
 name: product ion m/z delta
 def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI]

 is_a: MS:1001221 ! product ion attribute

 relationship: has_units MS:1000040 ! m/z

 
 [Term]
 id: MS:1000905
 name: percent of base peak times 100
 def: "The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries." [PSI:MS]
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000043 ! intensity unit
 
 [Term]
 id: MS:1000906
 name: peak intensity rank
 def: "Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc." [PSI:MS]
 xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
 is_a: MS:1000455 ! ion selection attribute
 relationship: part_of MS:1000231 ! peak
 
 [Term]
 id: MS:1000907
 name: peak targeting suitability rank
 def: "Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant." [PSI:MS]
 xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
 is_a: MS:1000455 ! ion selection attribute
 relationship: part_of MS:1000231 ! peak
 
 [Term]
 id: MS:1000908
 name: transition
 def: "A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely." [PSI:MS]
 synonym: "reaction" EXACT []
 relationship: part_of MS:1001458 ! spectrum generation information
 
 [Term]
 id: MS:1000909
 name: transition validation method
 def: "The strategy used to validate that a transition is effective." [PSI:MS]
 relationship: part_of MS:1000908 ! transition
 
 [Term]
 id: MS:1000910
 name: transition optimized on specified instrument
 def: "The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined." [PSI:MS]
 is_a: MS:1000909 ! transition validation method
 
 [Term]
 id: MS:1000911
 name: transition validated with an MS/MS spectrum on specified instrument

 def: "The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term." [PSI:MS]

 is_a: MS:1000909 ! transition validation method
 
 [Term]
 id: MS:1000912
 name: transition purported from an MS/MS spectrum on a different, specified instrument

 def: "The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad)." [PSI:MS]

 is_a: MS:1000909 ! transition validation method
 
 [Term]
 id: MS:1000913
 name: transition predicted by informatic analysis
 def: "The transition has been predicted by informatics software without any direct spectral evidence." [PSI:MS]
 is_a: MS:1000909 ! transition validation method
 
 [Term]
 id: MS:1000914

 name: tab delimited text format
 def: "A file format that has two or more columns of tabular data where each column is separated by a TAB character." [PSI:MS]

 is_a: MS:1001459 ! file format

 is_a: MS:1001040 ! intermediate analysis format

 
 [Term]
 id: MS:1000915
 name: retention time window attribute
 def: "An attribute of a window in time about which a peptide might elute from the column." [PSI:MS]
 relationship: part_of MS:1000894 ! retention time
 
 [Term]
 id: MS:1000916
 name: retention time window lower offset

 def: "The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000915 ! retention time window attribute
 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute
 
 [Term]
 id: MS:1000917
 name: retention time window upper offset

 def: "The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS]

 xref: value-type:xsd\:float "The allowed value-type for this CV term."
 is_a: MS:1000915 ! retention time window attribute
 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute
 
 [Term]
 id: MS:1000918
 name: target list
 def: "A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically." [PSI:MS]
 relationship: part_of MS:1001458 ! spectrum generation information
 
 [Term]
 id: MS:1000919
 name: target inclusion exclusion priority
 def: "A priority setting specifying whether included or excluded targets have priority over the other." [PSI:MS]
 relationship: part_of MS:1000918 ! target list
 
 [Term]
 id: MS:1000920
 name: includes supersede excludes
 def: "A priority setting specifying that included targets have priority over the excluded targets if there is a conflict." [PSI:MS]
 is_a: MS:1000919 ! target inclusion exclusion priority
 
 [Term]
 id: MS:1000921
 name: excludes supersede includes
 def: "A priority setting specifying that excluded targets have priority over the included targets if there is a conflict." [PSI:MS]
 is_a: MS:1000919 ! target inclusion exclusion priority
 
 [Term]
 id: MS:1000922
 name: Skyline

 def: "Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington." [https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default]

 is_a: MS:1000871 ! SRM software

 is_a: MS:1001139 ! quantitation software name

 
 [Term]
 id: MS:1000923
 name: TIQAM

 def: "Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/TIQAM/TIQAM.html]

 is_a: MS:1000871 ! SRM software
 
 [Term]
 id: MS:1000924
 name: MaRiMba

 def: "OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba]
 comment: This term was made obsolete because it was redundant with an existing term (MS:1000872).

 is_obsolete: true

 replaced_by: MS:1000872

 
 [Term]
 id: MS:1000925
 name: ATAQS
 def: "Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology." [PSI:MS]
 is_a: MS:1000871 ! SRM software
 
 [Term]
 id: MS:1000926
 name: product interpretation rank
 def: "The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1." [PSI:MS]
 xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."

 is_a: MS:1001221 ! product ion attribute

 
 [Term]
 id: MS:1000927
 name: ion injection time
 def: "The length of time spent filling an ion trapping device." [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:0000028 ! millisecond
 
 [Term]
 id: MS:1000928
 name: calibration spectrum
 def: "A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample." [PSI:MS]
 is_a: MS:1000559 ! spectrum type
 
 [Term]
 id: MS:1000929
 name: Shimadzu Biotech nativeID format

 def: "Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger." [PSI:MS]

 is_a: MS:1000767 ! native spectrum identifier format
 
 [Term]
 id: MS:1000930
 name: Shimadzu Biotech database entity
 def: "Shimadzu Biotech format." [PSI:MS]
 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1000931

 name: QTRAP 5500

 def: "Applied Biosystems|MDS SCIEX QTRAP 5500." [PSI:MS]

 is_a: MS:1000121 ! SCIEX instrument model

 
 [Term]
 id: MS:1000932

 name: TripleTOF 5600

 def: "SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS]
 is_a: MS:1000121 ! SCIEX instrument model

 [Term]
 id: MS:1000933
 name: protein modifications
 def: "Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000884 ! protein attribute
 
 [Term]
 id: MS:1000934
 name: gene name
 def: "Name of the gene from which the protein is translated." [PSI:MS]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1000884 ! protein attribute
 

 [Term]
 id: MS:1001000
 name: spectrum interpretation
 def: "Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra." [PSI:PI]
 relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
 
 [Term]
 id: MS:1001005

 name: SEQUEST:CleavesAt

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001006

 name: SEQUEST:ViewCV
 def: "SEQUEST View Input Parameters." [PSI:PI]
 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001007

 name: SEQUEST:OutputLines
 def: "Number of peptide results to show." [PSI:MS]

 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001009

 name: SEQUEST:DescriptionLines
 def: "Number of full protein descriptions to show for top N peptides." [PSI:MS]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001010
 name: de novo search
 def: "A de novo sequencing search (without database)." [PSI:PI]
 is_a: MS:1001080 ! search type
 
 [Term]
 id: MS:1001011
 name: search database details
 def: "Details about the database searched." [PSI:PI]
 is_a: MS:1001249 ! search input details
 
 [Term]
 id: MS:1001012
 name: database source

 def: "The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other)." [PSI:PI]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1001011 ! search database details
 
 [Term]
 id: MS:1001013
 name: database name
 def: "The name of the search database (nr, SwissProt or est_human)." [PSI:PI]
 is_a: MS:1001011 ! search database details
 
 [Term]
 id: MS:1001014
 name: database local file path
 def: "OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view." [PSI:PI]
 is_a: MS:1001011 ! search database details
 is_obsolete: true
 
 [Term]
 id: MS:1001015
 name: database original uri
 def: "URI, from where the search database was originally downloaded." [PSI:PI]
 xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
 is_a: MS:1001011 ! search database details
 
 [Term]
 id: MS:1001016
 name: database version

 def: "Version of the search database. In mzIdentML use the attribute instead." [PSI:PI]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1001011 ! search database details
 
 [Term]
 id: MS:1001017
 name: database release date
 def: "OBSOLETE: Use attribute in mzIdentML instead. Release date of the search database." [PSI:PI]
 is_a: MS:1001011 ! search database details
 is_obsolete: true
 
 [Term]
 id: MS:1001018
 name: database type
 def: "Database containing amino acid or nucleic acid sequences." [PSI:PI]
 is_a: MS:1001011 ! search database details
 
 [Term]
 id: MS:1001019
 name: database filtering
 def: "Was there filtering used on the database." [PSI:PI]
 is_a: MS:1001011 ! search database details
 
 [Term]
 id: MS:1001020
 name: DB filter taxonomy
 def: "A taxonomy filter was to the database search." [PSI:PI]
 is_a: MS:1001511 ! Sequence database filter types
 
 [Term]
 id: MS:1001021
 name: DB filter on accession numbers
 def: "Filtering applied specifically by accession number pattern." [PSI:PI]
 is_a: MS:1001511 ! Sequence database filter types
 
 [Term]
 id: MS:1001022
 name: DB MW filter
 def: "Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value." [PSI:PI]
 is_a: MS:1001511 ! Sequence database filter types
 
 [Term]
 id: MS:1001023
 name: DB PI filter
 def: "Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value." [PSI:PI]
 is_a: MS:1001511 ! Sequence database filter types
 
 [Term]
 id: MS:1001024
 name: translation frame

 def: "The translated open reading frames from a nucleotide database considered in the search (range: 1-6)." [PSI:PI]

 is_a: MS:1001011 ! search database details
 
 [Term]
 id: MS:1001025
 name: translation table
 def: "The translation table used to translate the nucleotides to amino acids." [PSI:PI]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_a: MS:1001011 ! search database details
 
 [Term]
 id: MS:1001026

 name: SEQUEST:NormalizeXCorrValues

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001027
 name: DB filter on sequence pattern
 def: "Filtering applied specifically by amino acid sequence pattern." [PSI:PI]
 is_a: MS:1001511 ! Sequence database filter types
 
 [Term]
 id: MS:1001028

 name: SEQUEST:SequenceHeaderFilter
 def: "String in the header of a sequence entry for that entry to be searched." [PSI:MS]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001029
 name: number of sequences searched
 def: "The number of sequences (proteins / nucleotides) from the database search after filtering." [PSI:PI]
 xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
 is_a: MS:1001011 ! search database details
 
 [Term]
 id: MS:1001030
 name: number of peptide seqs compared to each spectrum
 def: "Number of peptide seqs compared to each spectrum." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
 is_a: MS:1001011 ! search database details
 is_a: MS:1001405 ! spectrum identification result details
 
 [Term]
 id: MS:1001031
 name: spectral library search
 def: "A search using a library of spectra." [PSI:PI]
 is_a: MS:1001080 ! search type
 
 [Term]
 id: MS:1001032

 name: SEQUEST:SequencePartialFilter

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001035
 name: date / time search performed
 def: "OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run." [PSI:PI]
 is_a: MS:1001184 ! search statistics
 is_obsolete: true
 
 [Term]
 id: MS:1001036
 name: search time taken
 def: "The time taken to complete the search in seconds." [PSI:PI]
 xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
 is_a: MS:1001184 ! search statistics
 
 [Term]
 id: MS:1001037

 name: SEQUEST:ShowFragmentIons
 def: "Flag indicating that fragment ions should be shown." [PSI:MS]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001038

 name: SEQUEST:Consensus
 def: "Specify depth as value of the CVParam." [PSI:PI]

 xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."

 is_a: MS:1001006 ! SEQUEST:ViewCV

 
 [Term]
 id: MS:1001040
 name: intermediate analysis format

 def: "Type of the source file, the mzIdentML was created from." [PSI:PI]

 is_a: MS:1001459 ! file format
 
 [Term]
 id: MS:1001041

 name: SEQUEST:sortCV
 def: "SEQUEST View / Sort Input Parameters." [PSI:PI]
 is_a: MS:1001006 ! SEQUEST:ViewCV

 
 [Term]
 id: MS:1001042

 name: SEQUEST:LimitTo
 def: "Specify \"number of dtas shown\" as value of the CVParam." [PSI:PI]

 xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."

 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001044
 name: cleavage agent details
 def: "Details of cleavage agent (enzyme)." [PSI:PI]
 is_a: MS:1001249 ! search input details
 
 [Term]
 id: MS:1001045
 name: cleavage agent name
 def: "The name of the cleavage agent." [PSI:PI]
 is_a: MS:1001044 ! cleavage agent details
 
 [Term]
 id: MS:1001046

 name: SEQUEST:sort by dCn
 def: "Sort order of SEQUEST search results by the delta of the normalized correlation score." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001047

 name: SEQUEST:sort by dM
 def: "Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001048

 name: SEQUEST:sort by Ions

 def: "Sort order of SEQUEST search results given by the ions." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001049

 name: SEQUEST:sort by MH+

 def: "Sort order of SEQUEST search results given by the mass of the protonated ion." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001050

 name: SEQUEST:sort by P

 def: "Sort order of SEQUEST search results given by the probability." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001051
 name: multiple enzyme combination rules
 def: "OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any." [PSI:PI]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
 is_obsolete: true
 
 [Term]
 id: MS:1001052

 name: SEQUEST:sort by PreviousAminoAcid

 def: "Sort order of SEQUEST search results given by the previous amino acid." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001053

 name: SEQUEST:sort by Ref

 def: "Sort order of SEQUEST search results given by the reference." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001055
 name: modification parameters
 def: "Modification parameters for the search engine run." [PSI:PI]
 relationship: part_of MS:1001000 ! spectrum interpretation
 
 [Term]
 id: MS:1001056
 name: modification specificity rule
 def: "The specificity rules for the modifications applied by the search engine." [PSI:PI]
 is_a: MS:1001055 ! modification parameters
 
 [Term]
 id: MS:1001057
 name: tolerance on types
 def: "OBSOLETE: Tolerance on types." [PSI:PI]
 is_a: MS:1001055 ! modification parameters
 is_obsolete: true
 
 [Term]
 id: MS:1001058
 name: quality estimation by manual validation
 def: "The quality estimation was done manually." [PSI:PI]
 is_a: MS:1001060 ! quality estimation method details
 
 [Term]
 id: MS:1001059

 name: SEQUEST:sort by RSp

 def: "Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide)." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001060
 name: quality estimation method details

 def: "Method for quality estimation (manually or with decoy database)." [PSI:PI]

 is_a: MS:1001249 ! search input details
 
 [Term]
 id: MS:1001061
 name: neutral loss

 def: "OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD." [PSI:PI]

 is_a: MS:1001055 ! modification parameters
 is_obsolete: true

 replaced_by: MS:1000336

 
 [Term]
 id: MS:1001062

 name: Mascot MGF format
 def: "Mascot MGF file format." [PSI:MS]

 is_a: MS:1000560 ! mass spectrometer file format
 
 [Term]
 id: MS:1001065
 name: TODOscoring model

 def: "OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms." [PSI:PI]
 comment: This term was made obsolete and is replaced by the term (MS:1001961).

 is_a: MS:1001249 ! search input details

 is_obsolete: true
 replaced_by: MS:1001961

 
 [Term]
 id: MS:1001066
 name: ions series considered in search

 def: "The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI]

 is_a: MS:1001249 ! search input details
 
 [Term]
 id: MS:1001068

 name: SEQUEST:sort by Sp
 def: "Sort order of SEQUEST search results by the Sp score." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001069

 name: SEQUEST:sort by TIC

 def: "Sort order of SEQUEST search results given by the total ion current." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001070

 name: SEQUEST:sort by Scan

 def: "Sort order of SEQUEST search results given by the scan number." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001071

 name: SEQUEST:sort by Sequence

 def: "Sort order of SEQUEST search results given by the sequence." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001072

 name: SEQUEST:sort by Sf

 def: "Sort order of SEQUEST search results given by the SEQUEST result 'Sf'." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001073
 name: database type amino acid
 def: "Database contains amino acid sequences." [PSI:PI]
 is_a: MS:1001018 ! database type
 
 [Term]
 id: MS:1001079
 name: database type nucleotide

 def: "Database contains nucleic acid sequences." [PSI:PI]

 is_a: MS:1001018 ! database type
 
 [Term]
 id: MS:1001080
 name: search type

 def: "Enumeration of type of search value (i.e. from PMF, sequence tag, MS2)." [PSI:PI]

 is_a: MS:1001249 ! search input details
 
 [Term]
 id: MS:1001081
 name: pmf search
 def: "A peptide mass fingerprint search." [PSI:PI]
 is_a: MS:1001080 ! search type
 
 [Term]
 id: MS:1001082
 name: tag search
 def: "A sequence tag search." [PSI:PI]
 is_a: MS:1001080 ! search type
 
 [Term]
 id: MS:1001083
 name: ms-ms search

 def: "An MS2 search (with fragment ions)." [PSI:PI]

 is_a: MS:1001080 ! search type
 
 [Term]
 id: MS:1001084
 name: database nr

 def: "Non-redundant GenBank sequence database." [PSI:PI]

 is_a: MS:1001013 ! database name
 
 [Term]
 id: MS:1001085

 name: protein-level identification attribute

 def: "Protein level information." [PSI:PI]

 is_a: MS:1002694 ! single identification result attribute

 
 [Term]
 id: MS:1001086

 name: SEQUEST:sort by XCorr
 def: "Sort order of SEQUEST search results by the correlation score." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001087

 name: SEQUEST:ProcessCV
 def: "SEQUEST View / Process Input Parameters." [PSI:PI]
 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001088
 name: protein description
 def: "The protein description line from the sequence entry in the source database FASTA file." [PSI:PI]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1001085 ! protein-level identification attribute

 is_a: MS:1001342 ! database sequence details
 
 [Term]
 id: MS:1001089
 name: molecule taxonomy
 def: "The taxonomy of the resultant molecule from the search." [PSI:PI]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1001085 ! protein-level identification attribute

 is_a: MS:1001342 ! database sequence details
 is_a: MS:1001512 ! Sequence database filters
 
 [Term]
 id: MS:1001090
 name: taxonomy nomenclature
 def: "OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI]
 is_a: MS:1001089 ! molecule taxonomy
 is_obsolete: true

 replaced_by: MS:1001467
 replaced_by: MS:1001468
 replaced_by: MS:1001469
 replaced_by: MS:1001470

 
 [Term]
 id: MS:1001091
 name: NoEnzyme
 is_a: MS:1001045 ! cleavage agent name

 comment: This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956).
 is_obsolete: true

 
 [Term]
 id: MS:1001092

 name: peptide sequence-level identification statistic

 def: "Identification confidence metric for a peptide." [PSI:PI]

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 
 [Term]
 id: MS:1001093
 name: sequence coverage
 def: "The percent coverage for the protein based upon the matched peptide sequences (can be calculated)." [PSI:PI]
 xref: value-type:xsd\:decimal "The allowed value-type for this CV term."

 is_a: MS:1001085 ! protein-level identification attribute

 
 [Term]
 id: MS:1001094

 name: SEQUEST:sort by z

 def: "Sort order of SEQUEST search results given by the charge." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001041 ! SEQUEST:sortCV

 
 [Term]
 id: MS:1001095

 name: SEQUEST:ProcessAll

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001087 ! SEQUEST:ProcessCV

 
 [Term]
 id: MS:1001096

 name: SEQUEST:TopPercentMostIntense
 def: "Specify \"percentage\" as value of the CVParam." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001087 ! SEQUEST:ProcessCV

 
 [Term]
 id: MS:1001097
 name: distinct peptide sequences
 def: "This counts distinct sequences hitting the protein without regard to a minimal confidence threshold." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1001085 ! protein-level identification attribute

 
 [Term]
 id: MS:1001098
 name: confident distinct peptide sequences
 def: "This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1001085 ! protein-level identification attribute

 
 [Term]
 id: MS:1001099
 name: confident peptide qualification
 def: "The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1001085 ! protein-level identification attribute

 
 [Term]
 id: MS:1001100

 name: confident peptide sequence number

 def: "This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1001085 ! protein-level identification attribute

 
 [Term]
 id: MS:1001101

 name: protein group or subset relationship
 def: "Protein group or subset relationships." [PSI:PI]

 is_a: MS:1001085 ! protein-level identification attribute

 
 [Term]
 id: MS:1001102

 name: SEQUEST:Chromatogram

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001006 ! SEQUEST:ViewCV

 
 [Term]
 id: MS:1001103

 name: SEQUEST:InfoAndLog

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001006 ! SEQUEST:ViewCV

 
 [Term]
 id: MS:1001104

 name: database UniProtKB/Swiss-Prot
 def: "The name of the UniProtKB/Swiss-Prot knowledgebase." [PSI:PI]
 is_a: MS:1002126 ! database UniProtKB

 
 [Term]
 id: MS:1001105

 name: peptide sequence-level identification attribute

 def: "Peptide level information." [PSI:PI]

 is_a: MS:1002694 ! single identification result attribute

 
 [Term]
 id: MS:1001106

 name: SEQUEST:TopNumber
 def: "Specify \"number\" as value of the CVParam." [PSI:PI]

 xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."

 is_a: MS:1001087 ! SEQUEST:ProcessCV

 
 [Term]
 id: MS:1001107
 name: data stored in database
 def: "Source file for this mzIdentML was a data set in a database." [PSI:PI]
 is_a: MS:1001040 ! intermediate analysis format
 
 [Term]
 id: MS:1001108
 name: param: a ion

 def: "Parameter information, type of product: a ion with charge on the N-terminal side." [PSI:PI]

 is_a: MS:1002473 ! ion series considered in search

 
 [Term]
 id: MS:1001109

 name: SEQUEST:CullTo
 def: "Specify cull string as value of the CVParam." [PSI:PI]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1001087 ! SEQUEST:ProcessCV

 
 [Term]
 id: MS:1001110

 name: SEQUEST:modeCV
 def: "SEQUEST Mode Input Parameters." [PSI:PI]
 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001111

 name: SEQUEST:Full
 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
 is_a: MS:1001110 ! SEQUEST:modeCV

 
 [Term]
 id: MS:1001112
 name: n-terminal flanking residue

 def: "Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1003046 ! peptide-to-protein mapping attribute

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 
 [Term]
 id: MS:1001113
 name: c-terminal flanking residue

 def: "Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1003046 ! peptide-to-protein mapping attribute

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 
 [Term]
 id: MS:1001114
 name: retention time(s)

 def: "OBSOLETE Retention time of the spectrum from the source file." [PSI:PI]
 comment: This term was made obsolete because scan start time (MS:1000016) should be used instead.
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 relationship: has_units UO:0000010 ! second
 relationship: has_units UO:0000031 ! minute

 is_obsolete: true

 
 [Term]
 id: MS:1001115
 name: scan number(s)
 def: "OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData." [PSI:PI]

 comment: This former purgatory term was made obsolete.

 is_obsolete: true
 
 [Term]
 id: MS:1001116

 name: single protein identification statistic

 def: "Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group)." [PSI:PI]

 is_a: MS:1001085 ! protein-level identification attribute

 
 [Term]
 id: MS:1001117
 name: theoretical mass
 def: "The theoretical mass of the molecule (e.g. the peptide sequence and its modifications)." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 relationship: has_units UO:0000221 ! dalton
 
 [Term]
 id: MS:1001118
 name: param: b ion

 def: "Parameter information, type of product: b ion with charge on the N-terminal side." [PSI:PI]

 is_a: MS:1002473 ! ion series considered in search

 
 [Term]
 id: MS:1001119
 name: param: c ion

 def: "Parameter information, type of product: c ion with charge on the N-terminal side." [PSI:PI]

 is_a: MS:1002473 ! ion series considered in search

 
 [Term]
 id: MS:1001120

 name: SEQUEST:FormatAndLinks
 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
 is_a: MS:1001110 ! SEQUEST:modeCV

 
 [Term]
 id: MS:1001121
 name: number of matched peaks
 def: "The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 
 [Term]
 id: MS:1001122
 name: ions series considered

 def: "The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb)." [PSI:PI]

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 
 [Term]
 id: MS:1001123
 name: number of peaks used
 def: "The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 
 [Term]
 id: MS:1001124
 name: number of peaks submitted
 def: "The number of peaks from the original peaks listed that were submitted to the search engine." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 
 [Term]
 id: MS:1001125
 name: manual validation
 def: "Result of quality estimation: decision of a manual validation." [PSI:PI]
 xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1001092 ! peptide sequence-level identification statistic
 is_a: MS:1001116 ! single protein identification statistic

 
 [Term]
 id: MS:1001126

 name: SEQUEST:Fast
 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
 is_a: MS:1001110 ! SEQUEST:modeCV

 
 [Term]
 id: MS:1001127
 name: peptide sharing details
 def: "Accessions Containing Sequence - Accessions for each protein containing this peptide." [PSI:PI]

 is_a: MS:1001105 ! peptide sequence-level identification attribute

 
 [Term]
 id: MS:1001128

 name: SEQUEST:selectCV
 def: "SEQUEST Select Input Parameters." [PSI:PI]
 is_a: MS:1002096 ! SEQUEST input parameter

 
 [Term]
 id: MS:1001129
 name: quantification information
 def: "Quantification information." [PSI:PI]
 relationship: part_of MS:1001000 ! spectrum interpretation
 
 [Term]
 id: MS:1001130

 name: peptide raw area
 def: "OBSOLETE Peptide raw area." [PSI:PI]
 comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844).

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002737 ! peptide-level quantification datatype

 is_obsolete: true

 
 [Term]
 id: MS:1001131

 name: error on peptide area
 def: "Error on peptide area." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002737 ! peptide-level quantification datatype

 
 [Term]
 id: MS:1001132

 name: peptide ratio
 def: "Peptide ratio." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002737 ! peptide-level quantification datatype

 
 [Term]
 id: MS:1001133

 name: error on peptide ratio
 def: "Error on peptide ratio." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002737 ! peptide-level quantification datatype

 
 [Term]
 id: MS:1001134

 name: protein ratio
 def: "Protein ratio." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002738 ! protein-level quantification datatype

 
 [Term]
 id: MS:1001135

 name: error on protein ratio
 def: "Error on protein ratio." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002738 ! protein-level quantification datatype

 
 [Term]
 id: MS:1001136
 name: p-value (protein diff from 1 randomly)

 def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI]
 comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855).

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002738 ! protein-level quantification datatype

 is_obsolete: true

 
 [Term]
 id: MS:1001137

 name: absolute quantity
 def: "Absolute quantity in terms of real concentration or molecule copy number in sample." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
 is_a: MS:1001805 ! quantification datatype

 
 [Term]
 id: MS:1001138
 name: error on absolute quantity
 def: "Error on absolute quantity." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."
 is_a: MS:1001805 ! quantification datatype

 
 [Term]
 id: MS:1001139
 name: quantitation software name
 def: "Quantitation software name." [PSI:PI]
 is_a: MS:1000531 ! software
 is_a: MS:1001129 ! quantification information
 
 [Term]
 id: MS:1001140
 name: quantitation software version

 def: "OBSOLETE Quantitation software version." [PSI:PI]
 comment: This term was made obsolete because part of mzQuantML schema.

 is_a: MS:1001129 ! quantification information

 is_obsolete: true

 
 [Term]
 id: MS:1001141
 name: intensity of precursor ion
 def: "The intensity of the precursor ion." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."
 is_a: MS:1001805 ! quantification datatype

 
 [Term]
 id: MS:1001142
 name: database IPI_human

 def: "International Protein Index database for Homo sapiens sequences." [PSI:PI]

 is_a: MS:1001013 ! database name
 
 [Term]
 id: MS:1001143

 name: PSM-level search engine specific statistic

 def: "Search engine specific peptide spectrum match scores." [PSI:PI]

 is_a: MS:1002347 ! PSM-level identification statistic

 
 [Term]
 id: MS:1001144

 name: SEQUEST:SelectDefault
 is_a: MS:1001128 ! SEQUEST:selectCV

 
 [Term]
 id: MS:1001145

 name: SEQUEST:SelectAdvancedCV
 def: "SEQUEST Select Advanced Input Parameters." [PSI:PI]
 is_a: MS:1001128 ! SEQUEST:selectCV

 
 [Term]
 id: MS:1001146

 name: param: a ion-NH3 DEPRECATED
 def: "Ion a-NH3 parameter information, type of product: a ion with lost ammonia." [PSI:PI]

 is_a: MS:1001066 ! ions series considered in search
 
 [Term]
 id: MS:1001147
 name: protein ambiguity group result details

 is_a: MS:1001085 ! protein-level identification attribute

 is_a: MS:1001153 ! search engine specific score

 
 [Term]
 id: MS:1001148

 name: param: a ion-H2O DEPRECATED
 def: "Ion a-H2O if a significant and fragment includes STED." [PSI:PI]

 is_a: MS:1001066 ! ions series considered in search
 
 [Term]
 id: MS:1001149

 name: param: b ion-NH3 DEPRECATED
 def: "Ion b-NH3 parameter information, type of product: b ion with lost ammonia." [PSI:PI]

 is_a: MS:1001066 ! ions series considered in search
 
 [Term]
 id: MS:1001150

 name: param: b ion-H2O DEPRECATED
 def: "Ion b-H2O if b significant and fragment includes STED." [PSI:PI]

 is_a: MS:1001066 ! ions series considered in search
 
 [Term]
 id: MS:1001151

 name: param: y ion-NH3 DEPRECATED
 def: "Ion y-NH3 parameter information, type of product: y ion with lost ammonia." [PSI:PI]

 is_a: MS:1001066 ! ions series considered in search
 
 [Term]
 id: MS:1001152

 name: param: y ion-H2O DEPRECATED
 comment: This term was made obsolete - use MS:1001262 and MS:1002455 instead.

 is_a: MS:1001066 ! ions series considered in search
 
 [Term]
 id: MS:1001153
 name: search engine specific score
 def: "Search engine specific scores." [PSI:PI]

 is_a: MS:1002694 ! single identification result attribute

 
 [Term]
 id: MS:1001154

 name: SEQUEST:probability

 def: "The SEQUEST result 'Probability'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 
 [Term]
 id: MS:1001155

 name: SEQUEST:xcorr
 def: "The SEQUEST result 'XCorr'." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 relationship: has_order MS:1002108 ! higher score better

 
 [Term]
 id: MS:1001156

 name: SEQUEST:deltacn

 def: "The SEQUEST result 'DeltaCn'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 
 [Term]
 id: MS:1001157

 name: SEQUEST:sp

 def: "The SEQUEST result 'Sp' (protein)." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002363 ! search engine specific score for proteins

 
 [Term]
 id: MS:1001158

 name: SEQUEST:Uniq

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002363 ! search engine specific score for proteins

 
 [Term]
 id: MS:1001159

 name: SEQUEST:expectation value

 def: "The SEQUEST result 'Expectation value'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
 is_a: MS:1001153 ! search engine specific score
 
 [Term]
 id: MS:1001160

 name: SEQUEST:sf

 def: "The SEQUEST result 'Sf'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 
 [Term]
 id: MS:1001161

 name: SEQUEST:matched ions

 def: "The SEQUEST result 'Matched Ions'." [PSI:PI]
 xref: value-type:xsd\:integer "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 
 [Term]
 id: MS:1001162

 name: SEQUEST:total ions

 def: "The SEQUEST result 'Total Ions'." [PSI:PI]
 xref: value-type:xsd\:integer "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 
 [Term]
 id: MS:1001163

 name: SEQUEST:consensus score

 def: "The SEQUEST result 'Consensus Score'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
 is_a: MS:1001153 ! search engine specific score
 
 [Term]
 id: MS:1001164

 name: Paragon:unused protscore

 def: "The Paragon result 'Unused ProtScore'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002363 ! search engine specific score for proteins
 is_a: MS:1002368 ! search engine specific score for protein groups

 
 [Term]
 id: MS:1001165

 name: Paragon:total protscore

 def: "The Paragon result 'Total ProtScore'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002363 ! search engine specific score for proteins
 is_a: MS:1002368 ! search engine specific score for protein groups

 
 [Term]
 id: MS:1001166

 name: Paragon:score

 def: "The Paragon result 'Score'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002363 ! search engine specific score for proteins

 
 [Term]
 id: MS:1001167

 name: Paragon:confidence

 def: "The Paragon result 'Confidence'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002363 ! search engine specific score for proteins

 
 [Term]
 id: MS:1001168

 name: Paragon:expression error factor

 def: "The Paragon result 'Expression Error Factor'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002363 ! search engine specific score for proteins

 
 [Term]
 id: MS:1001169

 name: Paragon:expression change p-value

 def: "The Paragon result 'Expression change P-value'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002363 ! search engine specific score for proteins

 
 [Term]
 id: MS:1001170

 name: Paragon:contrib

 def: "The Paragon result 'Contrib'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1002363 ! search engine specific score for proteins

 
 [Term]
 id: MS:1001171

 name: Mascot:score

 def: "The Mascot result 'Score'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 
 [Term]
 id: MS:1001172

 name: Mascot:expectation value

 def: "The Mascot result 'expectation value'." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 
 [Term]
 id: MS:1001173

 name: Mascot:matched ions

 def: "The Mascot result 'Matched ions'." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 
 [Term]
 id: MS:1001174

 name: Mascot:total ions

 def: "The Mascot result 'Total ions'." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."

 is_a: MS:1001143 ! PSM-level search engine specific statistic

 
 [Term]
 id: MS:1001175
 name: peptide shared in multiple proteins

 def: "A peptide matching multiple proteins." [PSI:PI]

 is_a: MS:1001127 ! peptide sharing details
 
 [Term]
 id: MS:1001176
 name: (?<=[KR])(?\!P)

 def: "Regular expression for Trypsin." [PSI:PI]

 is_a: MS:1001180 ! Cleavage agent regular expression
 
 [Term]
 id: MS:1001177
 name: number of molecular hypothesis considered
 def: "Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search." [PSI:PI]
 xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
 is_a: MS:1001184 ! search statistics
 
 [Term]
 id: MS:1001178
 name: database EST

 def: "Expressed sequence tag nucleotide sequence database." [PSI:PI]

 is_a: MS:1001079 ! database type nucleotide
 
 [Term]
 id: MS:1001180
 name: Cleavage agent regular expression

 def: "Regular expressions for cleavage enzymes." [PSI:PI]

 relationship: part_of MS:1001044 ! cleavage agent details

 is_a: MS:1002479 ! regular expression

 
 [Term]
 id: MS:1001184
 name: search statistics
 def: "The details of the actual run of the search." [PSI:PI]
 is_a: MS:1001405 ! spectrum identification result details
 
 [Term]
 id: MS:1001189

 name: modification specificity peptide N-term
 def: "As parameter for search engine: apply the modification only at the N-terminus of a peptide." [PSI:PI]

 is_a: MS:1001056 ! modification specificity rule
 
 [Term]
 id: MS:1001190

 name: modification specificity peptide C-term
 def: "As parameter for search engine: apply the modification only at the C-terminus of a peptide." [PSI:PI]

 is_a: MS:1001056 ! modification specificity rule
 
 [Term]
 id: MS:1001191
 name: p-value

 def: "OBSOLETE Quality estimation by p-value." [PSI:PI]
 comment: This term was made obsolete because now is split into peptide and protein terms.

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001092 ! peptide sequence-level identification statistic

 is_a: MS:1001198 ! protein identification confidence metric
 is_obsolete: true

 
 [Term]
 id: MS:1001192
 name: Expect value
 def: "Result of quality estimation: Expect value." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001092 ! peptide sequence-level identification statistic
 is_a: MS:1001116 ! single protein identification statistic

 
 [Term]
 id: MS:1001193
 name: confidence score
 def: "Result of quality estimation: confidence score." [PSI:PI]
 xref: value-type:xsd\:double "The allowed value-type for this CV term."

 is_a: MS:1001092 ! peptide sequence-level identification statistic
 is_a: MS:1001116 ! single protein identification statistic

 
 [Term]
 id: MS:1001194
 name: quality estimation with decoy database
 def: "Quality estimation by decoy database." [PSI:PI]

 xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

 is_a: MS:1001060 ! quality estimation method details
 
 [Term]
 id: MS:1001195
 name: decoy DB type reverse
 def: "Decoy type: Amino acids of protein sequences are used in reverse order." [PSI:PI]
 is_a: MS:1001450 ! decoy DB details
 
 [Term]
 id: MS:1001196
 name: decoy DB type randomized
 def: "Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass)." [PSI:PI]
 is_a: MS:1001450 ! decoy DB details
 
 [Term]
 id: MS:1001197
 name: DB composition target+decoy
 def: "Decoy database composition: database contains original (target) and decoy entries." [PSI:PI]
 is_a: MS:1001450 ! decoy DB details
 
 [Term]
 id: MS:1001198

 name: protein identification confidence metric
 def: "Identification confidence metric for a protein." [PSI:PI]

 is_a: MS:1001116 ! single protein identification statistic

 
 [Term]
 id: MS:1001199

 name: Mascot DAT format
 def: "Source file for this mzIdentML was in Mascot DAT file format." [PSI:PI]

 is_a: MS:1001040 ! intermediate analysis format
 
 [Term]
 id: MS:1001200

 name: SEQUEST out file format
 def: "Source file for this mzIdentML was in SEQUEST out file format." [PSI:PI]

 is_a: MS:1001040 ! intermediate analysis format
 
 [Term]
 id: MS:1001201
 name: DB MW filter maximum

 def: "Maximum value of molecular weight filter." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."
 is_a: MS:1001512 ! Sequence database filters
 relationship: has_units UO:0000221 ! dalton
 relationship: has_units UO:0000222 ! kilodalton
 
 [Term]
 id: MS:1001202
 name: DB MW filter minimum

 def: "Minimum value of molecular weight filter." [PSI:PI]