Thank you Jimmy! I don't know that mgf files can be converted from mzXML. I have a perl script which can generate mgf files directly from thermo raw data. I searched these mgf files through mascot. Then under peptide summary report, these mascot search results can be output and formated as pep.xml files.
On Jun 29, 11:16 am, Jimmy Eng <jke...@gmail.com> wrote: > I would be a little concerned with "my files were transferred as xml > after mascot searching was done". What generated the xml files and in > what format are they? I believe that Mascot exported pep.xml files > won't run through the TPP correctly (but I could be wrong). > > The only advice I can give you is to follow the following steps to get > Mascot data analyze through the TPP: > - take your data and convert to mzXML > - generate mgf files from that mzXML > - search the mgf files through Mascot > - go bring back mascot search results in .dat format > - rename the .dat files to the same base name as mzXML > - convert the .dat to pep.xml > - use those pep.xml files as input to the PeptideProphet > > Any deviations from the above steps will only cause problems. > > > > On Mon, Jun 28, 2010 at 6:43 AM, chunchao <zc...@hotmail.com> wrote: > > It always give me an error message when I run PeptideProphet. My files > > were transferred as xml after mascot searching was done. The error > > message are as follows. Cound somebody tell me what's going on? Thank > > you in advance! > > > # Commands for session HMHX2UYYT on Wed May 26 12:03:21 2010 > > # BEGIN COMMAND BLOCK > > ###### BEGIN Command Execution ###### > > [Wed May 26 12:03:21 2010] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/ > > data; c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O > > c:/Inetpub/wwwroot/ISB/data/C1_trypsin_1.xml c:/Inetpub/wwwroot/ISB/ > > data/C1_trypsin_2.xml c:/Inetpub/wwwroot/ISB/data/C1_trypsin_3.xml c:/ > > Inetpub/wwwroot/ISB/data/C2_trypsin_1.xml > > OUTPUT: > > > c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 0, Build > > 200908071234 (MinGW)) > > > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/ > > Inetpub/wwwroot/ISB/data/C1_trypsin_1.xml" "c:/Inetpub/wwwroot/ISB/ > > data/C1_trypsin_2.xml" "c:/Inetpub/wwwroot/ISB/data/C1_trypsin_3.xml" > > "c:/Inetpub/wwwroot/ISB/data/C2_trypsin_1.xml" -L"7"" > > file 1: c:/Inetpub/wwwroot/ISB/data/C1_trypsin_1.xml > > file 2: c:/Inetpub/wwwroot/ISB/data/C1_trypsin_2.xml > > file 3: c:/Inetpub/wwwroot/ISB/data/C1_trypsin_3.xml > > file 4: c:/Inetpub/wwwroot/ISB/data/C2_trypsin_1.xml > > processed altogether 8267 results > > > results written to file c:/Inetpub/wwwroot/ISB/data/interact.pep.xml > > > direct your browser tohttp://localhost/ISB/data/interact.pep.shtml > > > command completed in 18 sec > > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > > MINPROB=0.05" > > (MASCOT) > > error: -1.0 homology score > > > command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > > MINPROB=0.05" failed: Operation not permitted > > > command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > > MINPROB=0.05" exited with non-zero exit code: 1 > > QUIT - the job is incomplete > > > command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O > > c:/Inetpub/wwwroot/ISB/data/C1_trypsin_1.xml c:/Inetpub/wwwroot/ISB/ > > data/C1_trypsin_2.xml c:/Inetpub/wwwroot/ISB/data/C1_trypsin_3.xml c:/ > > Inetpub/wwwroot/ISB/data/C2_trypsin_1.xml" failed: Operation not > > permitted > > END OUTPUT > > RETURN CODE:256 > > ###### End Command Execution ###### > > # All finished at Wed May 26 12:03:42 2010 > > # END COMMAND BLOCK > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to spctools-disc...@googlegroups.com. > > To unsubscribe from this group, send email to > > spctools-discuss+unsubscr...@googlegroups.com. > > For more options, visit this group > > athttp://groups.google.com/group/spctools-discuss?hl=en.- Hide quoted text - > > - Show quoted text - -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
