psidev-pi-dev

[Psidev-pi-dev] New version 4.1.22 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

[Psidev-pi-dev] New term needed for timsTOF Flex instrument

[Juan A. V. <ju...@eb...>]

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

Re: [Psidev-pi-dev] [Psidev-ms-dev] New term needed for timsTOF Flex instrument

[Eric D. <eri...@is...>]

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