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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/4fb17008-c00c-4f81-aee4-b5d0278dfe57%40googlegroups.com.
