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 to http://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 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 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.
