Hi- I finally figured out that if I do the mzXML conversion via the TPP prior to searching (rather than using MSConvert on another system), this seemed to make a difference in allowing TPP to process data correctly. So that solution is fixed. However, now I see a new issue. In older version of TPP, the NxS/T motif was colored in the ProteinProphet results if I indicated that prior to proteinprophet processing. Now, I can't get that button to work. I have it checked in the box at the top of the ProteinProphet output, but it won't highlight them or calculate the # of NxS/T peptides as it used to do. (I do a lot of N-glycopeptide capture).
Thanks! Rebekah On Mon, Feb 27, 2012 at 12:30 PM, Rebekah Dawson <[email protected]>wrote: > Hi- > Thanks for the response. I always have it set to "trypsin" when converting > the Sequest search results to pepXML within the TPP. Is there another place > to specify enzyme? I have the same boxes checked for peptideprophet that I > always used when going through the pipeline. One other thing I noticed was > that in this new version of TPP I have the option of doing a 'semi-enzyme' > process, which is actually what the original search is using. So I have now > tried doing the pepXML conversion with straight 'trypsin' or with this > extra 'semi' box checked also. Both of them create this failure. I have > also tried it with specifying the sequest.params file during pepXML > conversion or without specifying it, and get the same error either way. I > also don't understand where "MALDI mode" comes from in the log listed > below. I am not using MALDI data and I do not check the "MALDI data" box. > > Any help is much appreciated!! > R > > > On Mon, Feb 27, 2012 at 11:27 AM, [email protected] < > [email protected]> wrote: > >> Please try to rerun the pipeline once specifying the enzyme to see if >> that helps. >> >> Sent from my Android Device >> >> >> ----- Reply message ----- >> From: "Ruby" <[email protected]> >> To: "spctools-discuss" <[email protected]> >> Subject: [spctools-discuss] PeptideProphet error in 4.5.2 >> Date: Mon, Feb 27, 2012 7:02 am >> >> >> I have been using TPP 4.0 for over a year with no issues. Last week I >> upgraded to 4.5.2 and can't get PeptideProphet to work. I"m not doing >> anything in terms of how I proceed through the pipeline and what >> settings I use. I get the following error and I get it whether I try >> to do the pep.XML conversion in this version of TPP, or whether I use >> pepXML files generated using the previous version of TPP (and which >> worked fine in peptideprophet before). Any help would be much >> appreciated! >> >> Command 1 [Mon Feb 27 08:52:22 2012] [ Show / Hide ] >> >> run_in c:/Inetpub/wwwroot/ISB/data/Olaf/OR_8; c:\Inetpub\tpp-bin >> \xinteract -Now_8_1-3.pep.xml -p0.05 -l7 -OAgx -I1 - >> OT2_Gundry_2012-02-21_OR-08_1.pep.xml - >> OT2_Gundry_2012-02-21_OR-08_2.pep.xml - >> OT2_Gundry_2012-02-21_OR-08_3.pep.xml >> >> c:\Inetpub\tpp-bin\xinteract (TPP v4.5 RAPTURE rev 2, Build >> 201202031108 (MinGW)) >> >> running: "C:/Inetpub/tpp-bin/InteractParser "ow_8_1-3.pep.xml" -L"7"" >> processed altogether 0 results >> ERROR: output file created, c:/Inetpub/wwwroot/ISB/data/Olaf/OR_8/ >> ow_8_1-3.pep.xml, appears incomplete. Please check the input files for >> completeness. >> >> >> results written to file c:/Inetpub/wwwroot/ISB/data/Olaf/OR_8/ >> ow_8_1-3.pep.xml >> >> direct your browser to >> http://localhost/ISB/data/Olaf/OR_8/ow_8_1-3.pep.shtml >> >> >> >> command completed in 0 sec >> >> running: "C:/Inetpub/tpp-bin/DatabaseParser "ow_8_1-3.pep.xml"" >> command completed in 0 sec >> >> No single database specified (by -D option or in .pep.xml file). >> RefreshParser skipped. >> >> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "ow_8_1-3.pep.xml" >> MINPROB=0.05 ACCMASS GLYC EXCLUDE IGNORECHG=1 NEGGAMMA NONEGINIT >> DECOYPROBS RT EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT >> EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI >> LEAVE" >> using Accurate Mass Bins >> using RT >> using N-glyc info >> maldi mode >> Ignoring charge 1+ spectra. >> Using hardcoded values to initialize the distributions. >> Using Gamma Distribution to model the negative hits. >> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: >> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN >> >> Error: file update failed (did not find closing tag "</ >> msms_pipeline_analysis>"), check file ow_8_1-3.pep.xml.tmp.a04004 for >> completeness >> error: no peptideprophet data written to file ow_8_1-3.pep.xml >> >> command "C:/Inetpub/tpp-bin/PeptideProphetParser "ow_8_1-3.pep.xml" >> MINPROB=0.05 ACCMASS GLYC EXCLUDE IGNORECHG=1 NEGGAMMA NONEGINIT >> DECOYPROBS RT EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT >> EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI >> LEAVE" failed: Operation not permitted >> >> command "C:/Inetpub/tpp-bin/PeptideProphetParser "ow_8_1-3.pep.xml" >> MINPROB=0.05 ACCMASS GLYC EXCLUDE IGNORECHG=1 NEGGAMMA NONEGINIT >> DECOYPROBS RT EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT >> EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI >> LEAVE" exited with non-zero exit code: 1 >> QUIT - the job is incomplete >> >> command "c:\Inetpub\tpp-bin\xinteract -Now_8_1-3.pep.xml -p0.05 -l7 - >> OAgx -I1 -OT2_Gundry_2012-02-21_OR-08_1.pep.xml - >> OT2_Gundry_2012-02-21_OR-08_2.pep.xml - >> OT2_Gundry_2012-02-21_OR-08_3.pep.xml" failed: Operation not permitted >> >> Command FAILED >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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