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.
conditions.xml
Description: XML document
interact.pep.xml
Description: XML document
