Re: [Psidev-ms-dev] New version 3.50.0 of psi-ms.obo

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I'm a little slow noticing this (just now updating ProteoWizard's OBO), but
I wonder about the now obsoleted
id: MS:1001114
name: retention time(s)
def: "Retention time of the spectrum from the source file." [PSI:PI]

Surely chromatography and mass spec can happen in entirely different time
frames, as with MALDI - or am I misunderstanding something?

And how is it different from
id: MS:1000894
name: retention time
def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit the chromatographic column."
[PSI:MS]

And doesn't that definition have the same assumption about the column being
hooked up directly to the mass spec?

Cheers,
Brian Pratt

On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
Ger...@ru...> wrote:

> Dear proteomics community,
>
> attached there's the new version 3.50.0 of the psi-ms.obo file.
>
> It contains the changes concerning the retention time terms (issue 74),
> changes for the waters instrument term definitions and 3 new terms for the
> Byonic search engine.
>
>
> Changed CV terms in version 3.50.0 of psi-ms.obo:
> ==============================**===================
> ************ added the two is_a relations 'is_a: MS:1001105 ! peptide
> result details' and
> ************ 'is_a: MS:1001405 ! spectrum identification result details'
> [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:1001105 ! peptide result details
> is_a: MS:1001405 ! spectrum identification result details
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
>
> ************ Made obsolete
> [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 result details
> is_a: MS:1001405 ! spectrum identification result details
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
> is_obsolete: true
>
> ************ Changed the definition (removed 'peptide ...').
> [Term]
> id: MS:1000894
> name: retention time
> def: "A measure of the interval relative to the beginning of a mass
> spectrometric run." [PSI:MS]
> is_a: MS:1000887 ! peptide attribute
>
> ************ Changed the is_a relationship from 'detector type' --> 'array
> detector' for the next two terms
> [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: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
>
> ************ Added the 'is_a: MS:1000621 ! photodiode array detector'
> relationship
> [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
>
> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> relationship
> [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
>
> ************ Adapted the definitions for the following Waters instruments
> to be more specific and unambiguous:
> MS:1000159    GCT
> MS:1000170    M@LDI L
> MS:1000171    M@LDI LR
> MS:1000188    Q-Tof micro
> MS:1000189    Q-Tof ultima
> MS:1000191    quattro micro
> MS:1000192    Quattro UItima
> MS:1000632    Q-Tof Premier
> MS:1001761    ACQUITY UPLC
> MS:1001762    ACQUITY UPLC H-Class
> MS:1001763    ACQUITY UPLC H-Class Bio
> MS:1001764    ACQUITY UPLC I-Class
> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> MS:1001766    nanoACQUITY UPLC
> MS:1001767    nanoACQUITY UPLC System with Technology
> MS:1001768    nanoACQUITY UPLC with HDX Technology
> MS:1001769    TRIZAIC UPLC nanoTile
> MS:1001770    GCT Premier
> MS:1001771    MALDI Synapt G2 HDMS
> MS:1001772    MALDI Synapt G2 MS
> MS:1001773    MALDI Synapt G2-S HDMS
> MS:1001774    MALDI Synapt G2-S MS
> MS:1001775    MALDI Synapt HDMS
> MS:1001776    MALDI Synapt MS
> MS:1001777    Synapt G2 HDMS
> MS:1001778    Synapt G2 MS
> MS:1001779    Synapt G2-S HDMS
> MS:1001780    Synapt G2-S MS
> MS:1001781    Synapt HDMS
> MS:1001782    Synapt MS
> MS:1001783    Xevo G2 Q-Tof
> MS:1001784    Xevo G2 Tof
> MS:1001785    Xevo Q-Tof
> MS:1001786    3100
> MS:1001787    Acquity SQD
> MS:1001788    Acquity TQD
> MS:1001789    Quattro micro GC
> MS:1001790    Xevo TQ MS
> MS:1001791    Xevo TQD
> MS:1001792    Xevo TQ-S
> MS:1001795    Empower
> MS:1001796    Unify
>
>
> New CV terms in version 3.50.0 of psi-ms.obo:
> ==============================**===============
> [Term]
> id: MS:1002308
> name: fluorescence detector
> def: "A detector using a fluorescent signal after excitation with light."
> [PSI:MS]
> is_a: MS:1000026 ! detector type
>
> [Term]
> id: MS:1002309
> name: Byonic: Peptide AbsLogProb
> def: "The absolute value of the log-base10 of the Byonic posterior error
> probability (PEP) of the PSM. " [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for PSMs
> is_a: MS:1001153 ! search engine specific score
> has_order: MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002310
> name: Byonic: Protein AbsLogProb
> def: "The absolute value of the log-base10 of the Byonic posterior error
> probability (PEP) of the protein. " [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001116 ! single protein result details
> is_a: MS:1001153 ! search engine specific score
> has_order: MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002311
> name: Byonic: Peptide AbsLogProb2D
> def: "The absolute value of the log-base10 Byonic two-dimensional
> posterior error probability (PEP) of the PSM. The two-dimensional PEP takes
> into account protein ranking information as well as PSM information."
> [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for PSMs
> is_a: MS:1001153 ! search engine specific score
> has_order: MS:1002108 ! higher score better
>
> Best Regards,
> Gerhard
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatik / Biostatistik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.049a
> Universitätsstraße 150
> D-44801 Bochum
>  Phone: +49(0)234/32-21006
> Fax:    +49(0)234/32-14554
> Email:  Ger...@ru...
> Web:    http://www.medizinisches-**proteom-center.de<http://www.medizinisches-proteom-center.de>
>
>
>
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