You can continue using your perl script. To be as fully compatible with TPP tools as possible, have your perl script encode the same information in the TITLE line as MzXML2Search does. And test.
On Wed, Jun 30, 2010 at 1:06 PM, chunchao <[email protected]> wrote: > 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 <[email protected]> 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 <[email protected]> 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 [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.- 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 [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.
