mzIDentML

[2kl...@gmail.com]

Hi there,
I would like to convert PeptideProphet pep.XML (based on Comet Search) file to mzIdentML using tpp2mzid.
The command seems to work and the mzID file is generated but it is missing any fragmentation information.
I tried it on both Linux (Version 5.2.1) and Win (Version 5.2.0) and the results were similar.
The specific files that were tested were of peptides generated following non-specific cleavage (like MHC peptides) or of dimethylated ArgC peptides.
When I tried to convert the analysis of dimethylated peptides some error messages appeared saying:
Unknown xx modification: K = 162.158   5.07168
Unknown xx modification: n = 35.0709   122.015
Unknown xx modification: n = 29.0391   128.047
Unknown xx modification: K = 156.126   0.960137

If the pepXML include also Xpress information then an additional message appeared saying:
"WARNING: Unknown analysis_result: xpress"
Is there anything I can do to get it to work?
Many thanks,
OK

[Michael Hoopmann]

Hi,

 

I can shed some light on the mzIdentML support. Regarding the fragmentation information, it isn’t in the mzID file because it isn’t in the pepXML file. tpp2mzid can only convert values it is given as input.

 

The dimethylated peptide error messages might be only a minor concern indicating we need to update our mappings of modification masses to UNIMOD cvParams. What I believe is happening is that those modification masses in your mzID file are probably labeled as “unknown modification”. This should be, hopefully, just cosmetic until we update our UNIMOD referencing.

 

Hopefully someone else with more expertise in XPRESS can jump in and answer that question.

 

Cheers,

Mike

 

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[2kl...@gmail.com]

Thanks a lot Mike!

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