Re: [Psidev-ms-dev] psi-ms controlled vocabulary v.3.20.0 released

[Henk v. d. T. <h.w...@uu...>]

Dear community,

I'd like to discuss some CV parameters for the annotation of 
post-translational modification (PTM) scores. I'm working on a Proteome 
Discoverer plugin for Pride converter 2 (a DAO) for which I need these 
parameters. I couldn't find any appropriate terms for this, so I'm 
interested if something should be created.

The things I think should be stored are:
- The name of the algorithm (maybe with a version number). i.e. PTM 
score, a-score, h-score, pRS score, delta score, ...
- The score itself for each PTM

If I look at the psi-ms obo file, I was expecting this, score would be 
under 'peptide modification details' (MS:1001471), although I also found 
the 'peptide attribute' (MS:1000887) that also refers to modifications. 
Possibly somebody can shed some light on this?
Moreover, I would suggest the possibility to add PTM scores at the 
protein level (under 'protein modifications' MS:1000933) so future 
'compounded' scores can be addressed.

Does anybody have any thoughts on this?

Thanks, Henk

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*Henk van den Toorn, bioinformatician*
Biomolecular Mass Spectrometry and Proteomics Group
Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences
Utrecht University
Padualaan, 8
3584 CH Utrecht
The Netherlands

E-mail: h.w...@uu...
Tel: +31 30 253 6758
Fax: +31 30 253 6919
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