Hello Joseph, There is no support for the ProteomeDiscoverer pepXML file in the TPP. But the TPP comes with the open-source and free comet search engine, which should be comparable to sequest. However, if you are able to post your pepXML file I may be able to change the code to implement support in the TPP. If you are interested, please post your mzML (or raw) file, database, sequest parameters and pepXML somewhere on the cloud so I can grab them and use for a test case.
Cheers, -David On Mar 14, 2018 6:37 PM, "Joseph Gillen" <[email protected]> wrote: > Hello, > > I recently discovered TPP and have been trying to analyze my recent data > from Proteome Discoverer 2.2 with PeptideProphet and every time I try to > analyze the .pep.xml file that Proteome Discoverer exports I get the error > below. I've downloaded the tutorial set and that worked fine and if I > convert my RAW file to a mzXML and process it with Tandem then I can > analyze the .tandem.pep.xml file with PeptideProphet. Basically do I need > to reanalyze all my RAW files with Tandem or is it possible to export my > Sequest result to TPP? > > Thank you, > Joseph Gillen > > C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 > (Windows_NT-x86_64)) > PPM mode in Accurate Mass Model ... > running: "C:/TPP/bin/InteractParser > "/tmp/a06048/demo/tandem/interact.pep.xml" "171120_JG_4B_1.pep.xml" -L"7"" > file 1: 171120_JG_4B_1.pep.xml > > command "C:/TPP/bin/InteractParser "/tmp/a06048/demo/tandem/interact.pep.xml" > "171120_JG_4B_1.pep.xml" -L"7"" failed: Unknown error > > command "C:/TPP/bin/InteractParser "/tmp/a06048/demo/tandem/interact.pep.xml" > "171120_JG_4B_1.pep.xml" -L"7"" exited with non-zero exit code: -1073741819 > 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]. > 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. > -- 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.
