Thanks, Jimmy. Libra has completed successfully with the new mzXML files. I did have to follow your earlier instructions and first get MSFileReader3.0 before running ReAdW: http://proteomicsresource.washington.edu/protocols06/wine/ -Eric
On Monday, June 18, 2018 at 2:48:31 PM UTC-4, Jimmy Eng wrote: > > 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 <[email protected] <javascript:>> 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 [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
