Re: [spctools-discuss] MS3 quantification
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 > .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 > 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 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-discu...@googlegroups.com . >> To post to this group, send email to spctools...@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.
Re: [spctools-discuss] MS3 quantification
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 .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 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 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.
Re: [spctools-discuss] MS3 quantification
Cool! I will try that. Thank you so much, Jimmy! -Han On Tuesday, July 7, 2015 at 11:52:33 AM UTC-4, Jimmy Eng wrote: Libra, the TPP's tool for quantifying TMT/iTRAQ data, will now work with MS3 quantification. Make sure you're using the latest TPP and have this setting in your Libra condition file: reporterFromMS3 value=1 / On Tue, Jul 7, 2015 at 8:19 AM, hh1985 hh.ear...@gmail.com javascript: wrote: Hi all, I have some TMT10plex datasets using MS3 for quantification (MS2 for identification). Is there any tool that can analyze this type of data? Thanks a lot, -Han -- 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-discu...@googlegroups.com javascript:. To post to this group, send email to spctools...@googlegroups.com javascript:. Visit this group at http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
Re: [spctools-discuss] MS3 quantification
Libra, the TPP's tool for quantifying TMT/iTRAQ data, will now work with MS3 quantification. Make sure you're using the latest TPP and have this setting in your Libra condition file: reporterFromMS3 value=1 / On Tue, Jul 7, 2015 at 8:19 AM, hh1985 hh.earlyd...@gmail.com wrote: Hi all, I have some TMT10plex datasets using MS3 for quantification (MS2 for identification). Is there any tool that can analyze this type of data? Thanks a lot, -Han -- 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 http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
