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psi-ms.obo
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format-version: 1.2
data-version: 4.1.112
date: 08:02:2023 11:38
saved-by: Joshua Klein
auto-generated-by: OBO-Edit 2.3.1
import: http://purl.obolibrary.org/obo/pato.obo
import: http://purl.obolibrary.org/obo/stato.owl
default-namespace: MS
namespace-id-rule: * MS:$sequence(7,0,9999999)$
namespace-id-rule: * PEFF:$sequence(7,0,9999999)$
remark: coverage of namespace-id: MS:$sequence(7,4000000,4999999)$: Mass spectrometry quality control metrics
remark: namespace: MS
remark: namespace: PEFF
remark: coverage: Mass spectrometer output files and spectra interpretation
remark: creator: Yasset Perez-Riverol <yperez <-at-> ebi.ac.uk>
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: creator: Joshua Klein <jaklein <-at-> bu.edu>
remark: creator: Chris Bielow <chris.bielow <-at-> fu-berlin.de>
remark: creator: Wout Bittremieux <wbittremieux <-at-> health.ucsd.edu>
remark: creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de>
remark: creator: Julian Uszkoreit <julian.uszkoreit <-at-> ruhr-uni-bochum.de>
remark: creator: Mathias Walzer <walzer <-at-> ebi.ac.uk>
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: http://purl.obolibrary.org/obo/ms/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
[Typedef]
id: has_value_type
name: has value type
def: "'Entity A' has value type 'Entity B', such as xsd:float." []
[Typedef]
id: has_structured_representation_in_format
name: has structured representation in format
def: "The term is encoded in the structure of the named file format rather than as an explicit parameter, and should not be used as one in that format." []
[Typedef]
id: has_metric_category
name: has_metric_category
[Typedef]
id: has_value_concept
name: has_value_concept
[Typedef]
id: has_column
name: has_column
[Typedef]
id: has_optional_column
name: has_optional_column
[Term]
id: NCIT:C25330
name: Duration
def: "The period of time during which something continues." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
is_a: NCIT:C21514 ! Temporal Qualifier
[Term]
id: NCIT:C45781
name: Density
def: "The amount of something per unit size." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
is_a: NCIT:C25447 ! Characteristic
[Term]
id: NCIT:C68811
name: Cover
def: "Span a region or interval of distance, space or time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
is_a: NCIT:C25404 ! Action
[Term]
id: NCIT:C79083
name: Outlier
def: "An observation in a data set that is numerically distant from the rest of the data." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
is_a: NCIT:C20181 ! Conceptual Entity
[Term]
id: NCIT:C21514
name: Temporal Qualifier
def: "Terms used to indicate units of time or other terms associated with time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"}
is_a: NCIT:C41009 ! Qualifier
[Term]
id: NCIT:C41009
name: Qualifier
def: "A term that helps define and render a concept unique." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
synonym: "Modifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
synonym: "Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
is_a: NCIT:C20189 ! Property or Attribute
[Term]
id: NCIT:C25447
name: Characteristic
def: "The distinguishing qualities or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"}
synonym: "Characteristics" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
synonym: "Feature" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
synonym: "Features" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
is_a: NCIT:C20189 ! Property or Attribute
[Term]
id: NCIT:C20189
name: Property or Attribute
def: "A distinguishing quality or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"}
[Term]
id: NCIT:C25404
name: Action
def: "A thing done." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
subset: NCIT:C105763
synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
synonym: "Generic Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
is_a: NCIT:C43431 ! Activity
[Term]
id: NCIT:C43431
name: Activity
def: "An active process; excludes processes and mechanisms which fulfill biological functions." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 3.0.3"}
synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 5.3"}
synonym: "General activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
[Term]
id: NCIT:C20181
name: Conceptual Entity
def: "An organizational header for concepts representing mostly abstract entities." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
synonym: "Conceptual Entity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
[Term]
id: NCIT:C16847
name: Technique
def: "A practiced and regimented skill or series of actions." [] {http://purl.obolibrary.org/obo/NCIT_C16847="NCI"}
is_a: NCIT:C43431 ! Activity
[Term]
id: NCIT:C19044
name: Statistical Technique
def: "A method of analyzing or representing statistical data; a procedure for calculating a statistic." [] {http://purl.obolibrary.org/obo/NCIT_C19044="NCI"}
is_a: NCIT:C16847 ! Technique
[Term]
id: NCIT:C60694
name: Principal Component
def: "One of the axes representing the projection of varience resulting from principal component analysis." [] {http://purl.obolibrary.org/obo/NCIT_C60694="NCI"}
is_a: NCIT:C19044 ! Statistical Technique
[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]
is_a: MS:1000548 ! sample attribute
relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000002
name: sample name
def: "A reference string relevant to the sample under study." [PSI:MS]
is_a: MS:1000548 ! sample attribute
relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[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]
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000021 ! gram
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000005
name: sample volume
def: "Total volume of solution used." [PSI:MS]
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000098 ! milliliter
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000006
name: sample concentration
def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS]
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000175 ! gram per liter
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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]
is_a: MS:1000503 ! scan attribute
relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[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]
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units MS:1000040 ! m/z
relationship: has_units UO:0000169 ! parts per million
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000015
name: scan rate
def: "Rate in Th/sec for scanning analyzers." [PSI:MS]
is_a: MS:1000503 ! scan attribute
relationship: has_units MS:1000807 ! Th/s
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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]
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
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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]
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units UO:0000008 ! meter
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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.
relationship: has_units MS:1000040 ! m/z
is_obsolete: true
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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]
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[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 []
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units UO:0000228 ! tesla
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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]
is_a: MS:1000481 ! detector attribute
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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 []
is_a: MS:1000481 ! detector attribute
relationship: has_units UO:0000106 ! hertz
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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]
is_a: MS:1000496 ! instrument attribute
relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[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 []
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1000507 ! ion property
relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[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]
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
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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]
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000266 ! electronvolt
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[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]
is_a: MS:1000548 ! sample attribute
relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[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