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 From: spctools-discuss@googlegroups.com <spctools-discuss@googlegroups.com> On Behalf Of 2kl...@gmail.com Sent: Tuesday, February 04, 2020 1:28 PM To: spctools-discuss <spctools-discuss@googlegroups.com> Subject: [spctools-discuss] mzIDentML 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 spctools-discuss+unsubscr...@googlegroups.com <mailto:spctools-discuss+unsubscr...@googlegroups.com> . To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/4fb17008-c00c-4f81-aee4-b5d0278dfe57%40googlegroups.com <https://groups.google.com/d/msgid/spctools-discuss/4fb17008-c00c-4f81-aee4-b5d0278dfe57%40googlegroups.com?utm_medium=email&utm_source=footer> . -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/020501d5dba4%2463ee51a0%242bcaf4e0%24%40isbscience.org.
