Re: [Psidev-ms-dev] PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT

[Puneet S. <ps...@ch...>]

4:29 PM 4/16/2007


Terms that need debate:

- msLevel - The term appears as Precursor Ion Scan (PSI:1000100),  Product Ion Scan (PSI:1000101) and Nth Generation Product Ion (PSI:1000337). What term should we use for ms 4th, ms 5th and such? We have to keep precursor ion and product ion. Terms such as  daughter ion and parent ion are deprecated. We still use Fragment ion though. These are some additional related terms that I could find in the CV. 


[Term]
id: PSI:1000364
name: Fragment Ion
def: "A product ion resulting from the dissociation of a precursor ion." [PSI:GPS]
is_a: PSI:1000365 ! Ion

[Term]
id: PSI:1000344
name: Progeny Ion
def: "A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ ? M2+ ? M3+ ? M4+ ? M5+ M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+. " [PSI:GPS]
exact_synonym: "Progeny Fragment Ion" []
is_a: PSI:1000365 ! Ion

[Term]
id: PSI:1000342
name: Product Ion
def: "An ion formed as the product of a reaction involving a particular precursor ion. The reaction can unimolecular dissociation, an ion/molecule reaction, or involve simply a change in the number of charges. The terms daughter ion and parent ion are not recommended." [PSI:GPS]
is_a: PSI:1000365 ! Ion



- mzRangeStart, mzRangeStop
According to Eric it would be useful to have a start and stop rather than a single mass range which can be confusing. I think we need all three terms: mass range, mzRangeStart and mzRangeStop. Is there anyway to do that?

[Term]
id: PSI:1000313
name: Mass Range
def: "The limit of m/z over which a mass spectrometer can detect ions." [PSI:GPS]
is_a: PSI:1000444 ! m/z Separation Method


- I dont know what is this term for?:

[Term]
id: PSI:1000104
name: None
def: "None." [PSI:GPS]
is_a: PSI:1000021 ! Reflectron State


- Instrument Name

i think Instrument name is same as model because Instrument's model name is everything but the Vendor's name. Also, each instrument will be defined, such as LTQ-FT LTQ Orbitrap. The definition of each model would contain the vendor name. That means we are keeping Model as it is and Instrument Name will not be used?

[Term]
id: PSI:1000463
name: Instrument
def: "Device which performs a measurement." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology

[Term]
id: PSI:1000031
name: Model
def: "Instrument's model name (everything but the vendor's name)" [PSI:GPS]
relationship: part_of PSI:1000454 ! Instrument Additional Description


- Should we replace all ThermoFinnigan with Thermo Fisher Scientific because the company name has changed?



- LowestMzValue - Is this within a spectrum or within a experiment. A clear definition is needed. 

- HighestMzValue - Again what is the reference for this term. I have to know what is it for in order                    to get a clear definintion.  

- Scan Type - "Dictates the type of scan used to generate the spectrum. Usually refers to the range but can also include linked, precursor, product and neutral mass loss types of scan."

What is the difference between Scan Type and Scan Mode?

[Term]
id: PSI:1000036
name: Scan Mode
def: "TODO: Add definition." [PSI:GPS]
is_obsolete: true

















Terms to be added:


- We need to add:  LCQ Deca and LCQ Deca XP. Others are there. 

[Term]
id: PSI:1000169
name: LCQ Deca XP Plus
def: "ThermoFinnigan LCQ Deca XP Plus MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000168
name: LCQ Classic
def: "ThermoFinnigan LCQ Classic MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000167
name: LCQ Advantage
def: "ThermoFinnigan LCQ Advantage MS" [PSI:GPS]
is_a: PSI:1000031 ! Model


- Add InstrumentSerialNumber as a term. We are not using InstrumentIdentifier because serial number is unique.

- Add -FileFormatConversion as a term.




- MaldiSpotIdentifier - sample spot, analyte spot or MALDIspot would be a better term. 






















Terms whose definitions needs to be updated:

[Term]
id: PSI:1000441
name: Scan
def: "A function of the mass spectrometer in which it employs the mass analyzer to generate the mass spectrum of a range of ions or a specific ion" [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology

[Term]
id: PSI:1000036
name: Scan Mode
def: "TODO: Add definition." [PSI:GPS]
is_obsolete: true

-DataArrayContentType



[Term]
id: PSI:1000139
name: 4000 Q TRAP
def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000140
name: 4700 Proteomic Analyzer
def: "Applied Biosystems/MDS SCIEX 4700 Proteomic Analyzer MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000141
name: APEX IV
def: "Bruker Daltonics APEX IV MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000142
name: APEX-Q
def: "Bruker Daltonics APEX-Q MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000143
name: API 150EX
def: "Applied Biosystems/MDS SCIEX API 150EX MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000144
name: API 150EX Prep
def: "Applied Biosystems/MDS SCIEX API 150EX Prep MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000145
name: API 2000
def: "Applied Biosystems/MDS SCIEX API 2000 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000146
name: API 3000
def: "Applied Biosystems/MDS SCIEX API 3000 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000147
name: API 4000
def: "Applied Biosystems/MDS SCIEX API 4000 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000148
name: autoFlex II
def: "Bruker Daltonics autoFlex II MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000149
name: autoFlex TOF/TOF
def: "Bruker Daltonics autoFlex TOF/TOF MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000150
name: Auto Spec Ultima NT
def: "Waters AutoSpec Ultima NT MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000151
name: Bio TOF II
def: "Bruker Daltonics BioTOF II MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000152
name: Bio TOF Q
def: "Bruker Daltonics BioTOF Q MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000153
name: DELTA plusAdvantage
def: "ThermoFinnigan DELTAplusAdvantage MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000154
name: DELTAplusXP
def: "ThermoFinnigan DELTAplusXP MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000155
name: ELEMENT2
def: "ThermoFinnigan ELEMENT2 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000156
name: esquire4000
def: "Bruker Daltonics esquire4000 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000157
name: esquire6000
def: "Bruker Daltonics esquire6000 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000158
name: Explorer
def: "IonSpec Explorer MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000159
name: GCT
def: "Waters GCT MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000160
name: HCT
def: "Bruker Daltonics HCT MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000161
name: HCT Plus
def: "Bruker Daltonics HCTPlus MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000162
name: HiRes ESI
def: "IonSpec HiResESI MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000163
name: HiRes MALDI
def: "IonSpec HiResMALDI MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000164
name: IsoPrime
def: "Waters IsoPrime MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000165
name: IsoProbe
def: "Waters IsoProbe MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000166
name: IsoProbe T
def: "Waters IsoProbe T MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000167
name: LCQ Advantage
def: "ThermoFinnigan LCQ Advantage MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000168
name: LCQ Classic
def: "ThermoFinnigan LCQ Classic MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000169
name: LCQ Deca XP Plus
def: "ThermoFinnigan LCQ Deca XP Plus MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000170
name: M@LDI L
def: "Waters M@LDI L MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000171
name: M@LDI LR
def: "Waters M@LDI LR MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000172
name: MAT253
def: "ThermoFinnigan MAT253 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000173
name: MAT900XP
def: "ThermoFinnigan MAT900XP MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000174
name: MAT900XP Trap
def: "ThermoFinnigan MAT900XP Trap MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000175
name: MAT95XP
def: "ThermoFinnigan MAT95XP MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000176
name: MAT95XP Trap
def: "ThermoFinnigan MAT95XP Trap MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000177
name: microFlex
def: "Bruker Daltonics microFlex MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000178
name: microTOFLC
def: "Bruker Daltonics microTOFLC MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000179
name: Neptune
def: "ThermoFinnigan NEPTUNE MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000180
name: NG-5400
def: "Waters NG-5400 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000181
name: OMEGA
def: "IonSpec OMEGA MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000182
name: OMEGA-2001
def: "IonSpec OMEGA-2001 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000183
name: OmniFlex
def: "Bruker Daltonics OminFlex MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000184
name: Platform ICP
def: "Waters Platform ICP MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000185
name: PolarisQ
def: "ThermoFinnigan PolarisQ MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000186
name: Proteomics Solution 1
def: "Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000187
name: Q TRAP
def: "Applied Biosystems/MDS SCIEX Q TRAP MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000188
name: Q-Tof micro
def: "Waters Q-Tof micro MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000189
name: Q-Tof Ultima
def: "Waters Q-Tof Ultima MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000190
name: QSTAR
def: "Applied Biosystems/MDS SCIEX QSTAR MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000191
name: Quattro micro
def: "Waters Quattro micro MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000192
name: Quattro UItima
def: "Waters Quattro Uitima MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000193
name: Surveyor MSQ
def: "ThermoFinnigan Surveyor MSQ MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000194
name: SymBiot I
def: "Applied Biosystems/MDS SCIEX SymBiot I MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000195
name: SymBiot XVI
def: "Applied Biosystems/MDS SCIEX SymBiot XVI MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000196
name: TEMPUS TOF
def: "ThermoFinnigan TEMPUS TOF MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000197
name: TRACE DSQ
def: "ThermoFinnigan TRACE DSQ MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000198
name: TRITON
def: "ThermoFinnigan TRITON MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000199
name: TSQ QUANTUM
def: "ThermoFinnigan TSQ QUANTUM MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000200
name: Ultima
def: "IonSpec Ultima MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000201
name: ultraFlex
def: "Bruker Daltonics ultraFlex MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000202
name: ultraFlex TOF/TOF
def: "Bruker Daltonics ultraFlex TOF/TOF MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000203
name: Voyager-DE PRO
def: "Applied Biosystems/MDS SCIEX Voyager-DE PRO MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000204
name: Voyager-DE STR
def: "Applied Biosystems/MDS SCIEX Voyager-DE STR MS" [PSI:GPS]
is_a: PSI:1000031 ! Model

[Term]
id: PSI:1000441
name: Scan
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology

[Term]
id: PSI:1000442
name: Spectrum
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology

[Term]
id: PSI:1000443
name: Mass Analyzer
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology

[Term]
id: PSI:1000444
name: m/z Separation Method
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology

[Term]
id: PSI:1000445
name: Sequential m/z Separation Method
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology

[Term]
id: PSI:1000036
name: Scan Mode
def: "TODO: Add definition." [PSI:GPS]
is_obsolete: true


[Term]
id: PSI:1000127
name: Centroid Mass Spectrum
def: "TODO: Add definition." [PSI:GPS]
is_a: PSI:1000035 ! Peak Processing

[Term]
id: PSI:1000128
name: Continuum Mass Spectrum
def: "TODO: Add definition." [PSI:GPS]
is_a: PSI:1000035 ! Peak Processing


[Term]
id: PSI:1000131
name: Number Of Counts
def: "TODO: Add definition." [PSI:GPS]
is_a: PSI:1000043 ! Intensity Unit

[Term]
id: PSI:1000132
name: Percent Of Base Peak
def: "TODO: Add definition." [PSI:GPS]
is_a: PSI:1000043 ! Intensity Unit


[Term]
id: PSI:1000138
name: Percent
def: "TODO: Add definition." [PSI:GPS]
is_a: PSI:1000046 ! Energy Unit


[Term]
id: PSI:1000441
name: Scan
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology

[Term]
id: PSI:1000442
name: Spectrum
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology


[Term]
id: PSI:1000443
name: Mass Analyzer
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology


[Term]
id: PSI:1000444
name: m/z Separation Method
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology

[Term]
id: PSI:1000445
name: Sequential m/z Separation Method
def: "TODO: Add definition." [PSI:GPS]
relationship: part_of PSI:0000000 ! mzOntology









Terms we decided not to add:


- AnalyteIdentifier - same as Sample Name (PSI:1000002), and/or Sample

Number (PSI:1000001)

- BasePeakMz - same as Base Peak, PSI:1000210


- InstrumentIdentifier. Same as InstrumentSerialNumber.