We can use the SQT format, not the SRF format. Convert to SQT, upload your SQTfile using instructions in the link I sent. We can adjust PeptideProphet to recognize this version of sequest, which reports a different search engine name in the pepXML format.
On Tue, Jun 28, 2011 at 3:07 PM, Kinfai Au <[email protected]> wrote: > If I start with SRF file, what could I do to run the peptideprophet? > > On Jun 22, 10:37 am, David Shteynberg > <[email protected]> wrote: >> Hi Kinfai, >> >> The problem lies in the error message: >> (mspire: ms-sequest >> not recognizedspire: ms-sequest) >> >> We have not processed this sort of data yet. If you want to post your >> file here we can adjust the TPP to deal with these files in the >> future: >> >> http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_A... >> >> Thanks, >> -David >> >> >> >> >> >> >> >> On Wed, Jun 22, 2011 at 12:00 AM, Kinfai Au <[email protected]> wrote: >> > After converting SQT file to pep.xml file, I ran the following >> > command: >> >> > xinteract -Ninteract.pep.xml -p0.05 -l7 -O test5.pep.xml >> >> > Then, it crashed in some step. Here is the error message. I spent days >> > on it but the pipeline TPP still fails. Could anyone give me some >> > help? >> > ################################################################ >> >> > xinteract (TPP v4.4 VUVUZELA rev 1, Build 201106201323 (linux)) >> >> > running: "/home/stow/swtree/stow/TPP-4.4.1/bin/InteractParser >> > 'interact.pep.xml' 'test5.pep.xml' -L'7'" >> > file 1: test5.pep.xml >> > processed altogether 41651 results >> >> > results written to file /home/kinfai/test5/interact.pep.shtml >> >> > command completed in 44 sec >> >> > running: "/home/stow/swtree/stow/TPP-4.4.1/bin/PeptideProphetParser >> > 'interact.pep.xml' MINPROB=0.05" >> > )(mspire: ms-sequest >> > not recognizedspire: ms-sequest >> >> > command "/home/stow/swtree/stow/TPP-4.4.1/bin/PeptideProphetParser >> > 'interact.pep.xml' MINPROB=0.05" 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 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 >> > athttp://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. 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.
