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From: mayerg97 <ger...@ru...> - 2019-01-25 13:32:36
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Dear proteomics/metabolomics community, the new version 4.1.22 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo New CV terms in version 4.1.22 of psi-ms.obo: ============================================= [Term] id: MS:1003004 name: maXis II def: "Bruker Daltonics' maXis II." [PSI:MS] is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1003005 name: timsTOF Pro def: "Bruker Daltonics' timsTOF Pro." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1003006 name: mean inverse reduced ion mobility array def: "Array of inverse reduced ion mobilities, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002893 ! ion mobility array relationship: has_units MS:1002814 ! volt-second per square centimeter [Term] id: MS:1003007 name: raw ion mobility array def: "Array of raw drift times." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second [Term] id: MS:1003008 name: raw inverse reduced ion mobility array def: "Array of raw inverse reduced ion mobilities." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002893 ! ion mobility array relationship: has_units MS:1002814 ! volt-second per square centimeter [Term] id: MS:1003009 name: Shimadzu Biotech LCD format def: "Shimadzu Biotech LCD file format." [PSI:PI] is_a: MS:1000560 ! mass spectrometer file format [Term] id: PEFF:0001035 name: initiator methionine def: "N-terminal methionine residue of a protein that can be co-translationally cleaved." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! regular expression for each VariantSimple item Changed CV terms in version 4.1.22 of psi-ms.obo: ================================================= ************ "volt-second per square centimeter" ************ --> volt-second per square centimeter [Term] id: MS:1002815 name: inverse reduced ion mobility def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute is_a: MS:1002892 ! ion mobility attribute relationship: has_units MS:1002814 ! volt-second per square centimeter ************ Removed relationship: has_units MS:1002814 ! volt-second per square centimeter [Term] id: MS:1002816 name: mean ion mobility array def: "Array of drift times, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second ************ MS:1002901 ! search engine specific score for proteoforms ************ --> MS:1002906 ! search engine specific score for proteoforms [Term] id: MS:1002930 name: TopPIC:proteoform-level FDR def: "TopPIC proteoform-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002906 ! search engine specific score for proteoforms [Term] id: MS:1002952 name: TopMG:proteoform-level FDR def: "TopMG proteoform-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002906 ! search engine specific score for proteoforms Best Regards, Gerhard -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Scientific assistant* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail *ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Juan A. V. <ju...@eb...> - 2020-03-05 11:46:03
Attachments:
smime.p7s
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Dear all, We have a submitter that has generated data coming from an timsTOF fleX instrument. This term is not yet in the PSI MS CV. The one that is there is for the timsTOF Pro (MS:1003005). So I am proposing to add it to the CV. [Term] id: MS:1xxxxx name: timsTOF fleX def: "Bruker Daltonics' timsTOF fleX." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model Thanks in advance, Juan |
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From: Eric D. <eri...@is...> - 2020-03-05 16:57:27
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I don’t know much about this instrument itself, but seems reasonable to me. My only suggested change is to remove the apostrophe. It is incorrectly used and unnecessary. But I also notice that all Bruker instruments have this (so Juan was just following the pattern, okay). But I vote that we fix this everywhere in the CV. i.e. s/Daltonics’/Daltonics/g Thermo doesn’t have apostrophes, Waters doesn’t have apostrophes. I assume the intent was to imply a possessive, but I propose we strip that for all Bruker models. It’s only in the definition anyway, so should not affect software. Thanks, Eric *From:* Juan Antonio Vizcaino <ju...@eb...> *Sent:* Thursday, March 5, 2020 3:46 AM *To:* psi...@li... *Cc:* psi...@li...; Mass spectrometry standard development <psi...@li...>; Deepti Jaiswal Kundu < ja...@eb...> *Subject:* [Psidev-ms-dev] New term needed for timsTOF Flex instrument Dear all, We have a submitter that has generated data coming from an timsTOF fleX instrument. This term is not yet in the PSI MS CV. The one that is there is for the timsTOF Pro (MS:1003005). So I am proposing to add it to the CV. [Term] id: MS:1xxxxx name: timsTOF fleX def: "Bruker Daltonics' timsTOF fleX." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model Thanks in advance, Juan |