Eric, Unfortunately the Libra's MS3 TMT support is based on an optional "filterLine" attribute in the mzXML file that msconvert does not write out as far as I'm aware. Libra uses the information in the filter line to identify the ms3 scan number associated with the ms2 scan.
As a workaround, you can grab the ReAdW Thermo to mzXML converter here: https://github.com/PedrioliLab/ReAdW/blob/master/bin/ReAdW.2016010.msfilereader.exe Place it in a directory with your raw file. Drag the raw file on to the binary to start a conversion. Or if you prefer running on the command line in a CMD window, the command would be: ReAdW.2016010.msfilereader.exe <yourrawfile>.raw Use the generated mzXML in place of the one created by msconvert and try running Libra again. On Mon, Jun 18, 2018 at 10:44 AM <chanye...@gmail.com> wrote: > Hi all, > > I'm learning to process SPS-MS3 TMT data using Libra. > The comet-ms group has helped sort out my search issue ( > https://groups.google.com/forum/#!topic/comet-ms/lJ88p_Loc0s) > > For Libra, I've already added the line <reportFromMS3 value="1"/> to the > conditions.xml file. > > However, I seem to be having trouble with the LibraPeptideParser, when > submitting a job (xinteract -Lconditions.xml -Op *.pep.xml) > As shown at the bottom, I think PeptideProphet was able to complete its > steps. > > However, as soon as Libra starts, I keep running into Error ms2 filter > line: > Not sure if it matters, but I used ProteoWizard/msconver to make the mzXML > files (just default parameters, without special options). > I've also trimmed my interact.pep.xml down to the first 1000 lines, in > case there's anything in there I might have overlooked. > > Thanks in advance for your advice. > -Eric > > > Parsing search results "/cluster/inbox/20180611_AM15 (Comet)"... > => Found 5075 hits. (780 decoys, 0 excluded) > => Total so far: 100662 hits. (13440 decoys, 0 excluded) > command completed in 5 sec > > running: "/cluster/app/TPP/5.1.0/bin/LibraPeptideParser 'interact.pep.xml' > -cconditions.xml" > LibraPeptideParser (TPP v5.1.0 Syzygy, Build 201803201443-exported > (Linux-x86_64)) > Calculating and updating peptide ratios in interact.pep.xml... > Error ms2 filter line: > > > command "/cluster/app/TPP/5.1.0/bin/LibraPeptideParser 'interact.pep.xml' > -cconditions.xml" exited with non-zero exit code: 256 > QUIT - the job is incomplete > > > -- > 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 post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.