Re: [Psidev-pi-dev] [Psidev-ms-dev] List of ion species, anyone ?

[Schober, D. <dsc...@ip...>]

Dear all,

  First, my admittedly picky view on the matter, having my formal 
ontology hat on (which I wear less and less often these days) ...

Aside my usual ontological aversions against epistemic intrusion a la 
M+3H *ion* /is_a/ *search input details* (rather than a molecule/ion), I 
think the presented pattern will do, given the pragmatic mz CV design. 
Another design principle I am not really comfortable with is that the 
essentials of a class are captured in the definition by selected 
extrinsic rather than essential intrinsic properties, i.e. in this case 
that Ion classes like "positive mode adduct ion type" are defined via 
the mode of an Instrument-run that detected them ("Adduct ion type from 
positive ion mode."). A more intrinsic definition would be via the 
ionisation level of the adduct itself.

These are just comments, and Gerhard knows the CV structure and design 
principles much better.

Best regards,

    Daniel Schober


Am 09.06.2017 um 10:41 schrieb mayerg97:
> Hi Joel and Steffen,
> dear metabolomics and proteomics community,
>
> would the following terms fit for you purposes?
>
> [Term]
> id: MS:1002806
> name: adduct ion type
> def: "Adduct ion type resulting from ionization in ESI-MS or other 
> soft ionization techniques." [PSI:MS]
> is_a: MS:1001249 ! search input details
>
> [Term]
> id: MS:1002807
> name: positive mode adduct ion type
> def: "Adduct ion type from positive ion mode." [PSI:MS]
> is_a: MS:1002806 ! adduct ion type
>
> [Term]
> id: MS:1002808
> name: negative mode adduct ion type
> def: "Adduct ion type from negative ion mode." [PSI:MS]
> is_a: MS:1002806 ! adduct ion type
>
> [Term]
> id: MS:1002809
> name: M+3H ion
> def: "M+3H ion in positive ion mode (M in the property ionMass denotes 
> the mass of the neutral molecule)." 
> [http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator, 
> http://dx.doi.org/10.1016/S1044-0305(99)00089-6]
> property_value: ionMass: "M/3 + 1.007276" xsd:string
> is_a: MS:1002807 ! positive mode adduct ion type
>
> ... analogous for the other positive mode adduct ions
>
> [Term]
> id: MS:10028xy
> name: M-3H ion
> def: "M-3H ion in negative ion mode (M in the property ionMass denotes 
> the mass of the neutral molecule)." 
> [http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator, 
> http://dx.doi.org/10.1016/S1044-0305(99)00089-6]
> property_value: ionMass: "M/3 - 1.007276 " xsd:string
> is_a: MS:1002808 ! negative mode adduct ion type
>
> ... analogous for the other negative mode ions
>
> Best regards,
> Gerhard Mayer
>
> Am 05.01.2017 um 13:08 schrieb Joel Rein:
>> Hi Steffen,
>>
>> I'd be very keen to see such a list developed/help with the RFC.
>> I think Tobias Kind's list 
>> (http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/) 
>> would be a useful list to include.
>>
>> Cheers,
>> Joel
>>
>> On Wednesday, January 4, 2017 at 8:06:12 PM UTC, Steffen Neumann wrote:
>>
>>     Hi,
>>
>>     are there any efforts to collect ion species for psi-ms.obo,
>>     such as [M+H]+ or [M-Cl]- ?
>>
>>     I was able to find "(M+H)+" in [1], but nothing in psi-ms.obo.
>>     I know a few groups interested in such a list, and would be
>>     happy to collect terms and send a proposal to Gerhard for inclusion.
>>
>>     If there are no proposals or suggestions, I would start-off
>>     the stuff Michael Witting has collected, and come back with an RFC.
>>
>>     Yours,
>>     Steffen
>>
>>
>>     [1]
>>     http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051
>>     <http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051>
>>
>>
>>
>>
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>
> -- 
>
> *--------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *PhD student*
>
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>
> *DEPARTMENT Medical Bioinformatics*
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>

-- 

Dr. Daniel Schober
Senior Ontologist, Data manager

Leibniz Institute of Plant Biochemistry, http://www.IPB-Halle.de
Dept. for Stress and Developmental Biology Bioinformatics & Mass Spectrometry
Weinberg 3 Tel. +49 (0) 345 5582 - 1476
06120 Halle