Thanks a lot Mike!
On Tuesday, February 4, 2020 at 11:45:22 PM UTC+2, Michael Hoopmann wrote: > > 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:* [email protected] <javascript:> < > [email protected] <javascript:>> *On Behalf Of * > [email protected] <javascript:> > *Sent:* Tuesday, February 04, 2020 1:28 PM > *To:* spctools-discuss <[email protected] <javascript:>> > *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 [email protected] <javascript:>. > 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/29cd03aa-12a7-4ff4-8f87-bfef4657689e%40googlegroups.com.
