Hi Brian, I ran the Mascot search again with "trypsin" as enzyme, instead of tryspin/P. The .dat file was able to convert to .pep.xml file successfully (cool!). Well, there is a warning at the end of the command lines, and I don't know how important this is.
"....... 333. opening 334spectrum.0000.0000.3.out warning: cannot open "c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.mzXML" for reading MS instrument info. *Command Successful"* When I ran "Analyze Peptides" for the next step, It failed. It seemed can't find .mzXML file (MS data?). There is the mzXML file in the same folder. see following error message: # Commands for session NYDW4ZIZ7 on Mon Jun 28 16:24:38 2010 # BEGIN COMMAND BLOCK ###### BEGIN Command Execution ###### [Mon Jun 28 16:24:38 2010] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data/SSM411; c:\Inetpub\tpp-bin\xinteract -NSSM411.pep.xml -p0.05 -l1 -Oi -X-m1.0-nC,9.0 -A-lC-r0.5-mC9.0 c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.pep.xml OUTPUT: c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "SSM411.pep.xml" "c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.pep.xml" -L"1"" file 1: c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.pep.xml processed altogether 238 results results written to file c:/Inetpub/wwwroot/ISB/data/SSM411/SSM411.pep.xml direct your browser to http://localhost/ISB/data/SSM411/SSM411.pep.shtml command completed in 0 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "SSM411.pep.xml" MINPROB=0.05 ICAT" (MASCOT) (icat) results for charge 1: 0 id tot and 0 adj scores results for charge 2: 189 id tot and 55 adj scores results for charge 2: 21.2543 adj_ion_mean and 25.4733 adj_ion_hom mean 23.7547id mean0.908354 correlation (r) 2+ ion - id = 0.988351*(ion - hom) + -3.92233 with error = 4.05281 mean ion - id: 21.2543, mean ion - hom: 25.4733 results for charge 3: 49 id tot and 16 adj scores results for charge 4: 0 id tot and 0 adj scores results for charge 5: 0 id tot and 0 adj scores results for charge 6: 0 id tot and 0 adj scores results for charge 6: -0 adj_ion_mean and -0 adj_ion_hom mean 0id meannan correlation (r) results for charge 7: 0 id tot and 0 adj scores init with MASCOT trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) akel...@isb read in 0 1+, 188 2+, 49 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: .........10.........20.... model complete after 25 iterations command completed in 0 sec running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i SSM411.pep.xml" Analyzing SSM411.pep.xml ... Parsing search results "c:/Inetpub/wwwroot/ISB/data/SSM411/F030382 (MASCOT)"... => Total of 154 hits. command completed in 1 sec running: "C:/Inetpub/tpp-bin/XPressPeptideParser "SSM411.pep.xml" -m1.0 -nC,9.0" WARNING: Found more than one variable mod on 'C'. XPRESS error - cannot open file from basename c:/Inetpub/wwwroot/ISB/data/SSM411/F030382, will try to derive from scan names scan-derived scan file c:/Inetpub/wwwroot/ISB/data/SSM411/.mzXML (from ) not found, cannot proceed... command "C:/Inetpub/tpp-bin/XPressPeptideParser "SSM411.pep.xml" -m1.0 -nC,9.0" failed: Operation not permitted command "C:/Inetpub/tpp-bin/XPressPeptideParser "SSM411.pep.xml" -m1.0 -nC,9.0" exited with non-zero exit code: 1 QUIT - the job is incomplete command "c:\Inetpub\tpp-bin\xinteract -NSSM411.pep.xml -p0.05 -l1 -Oi -X-m1.0-nC,9.0 -A-lC-r0.5-mC9.0 c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.pep.xml" failed: Operation not permitted END OUTPUT RETURN CODE:256 ###### End Command Execution ###### # All finished at Mon Jun 28 16:24:39 2010 # END COMMAND BLOCK Any suggestion for fixing this? Thanks in advance Jing On Thu, Jun 24, 2010 at 8:06 AM, Brian Pratt <[email protected]>wrote: > Not everyone has read access to the ISB's FTP server (including me), which > is why I said "upload your new mascot result file to the files area at > http://groups.google.com/group/spctools-discuss?hl=en. " > > Anyway, there are two problems: > 1) 'error: enzyme in search constraint "Trypsin/P" is not recognized' > 2) the above message doesn't appear by default and the program fails > silently > > I'll check in a fix for the second problem. > -- 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.
