When charge states are not listed in the mzXML file you should run the command:
MzXML2Search -mgf -c1-3 *.mzXML This will generate the mgf files to submit to Mascot. Once you get the .dat files back you should rename that to the original basename of the mzXML file with the .dat extension. Now you should run Mascot2XML and the scan numbers should be ok. -David On Mon, Jun 28, 2010 at 5:10 PM, Jimmy Eng <[email protected]> wrote: > Unfortunately based on the error messages, I don't believe that > naming/renaming the mzXML will solve all of the problems. > > One convention to try and stick to is to use the same base name for > all of the files. That means either > F030382.dat, F030382.pep.xml, F030382.mzXML > or > SSM411.dat, SSM411.pep.xml, SSM411.mzXML > or better yet > original_name.mzXML, original_name.dat, original_name.pep.xml (where > you keep the base name the same as the original mzXML base name). > > Sorry if I'm mixing up those two file base names but I see references > to pep.xml files for both. > > I see you're trying to run XPRESS quantitation and it look like it's > reading an empty base name (to which it appends ".mzXML" to find > corresponding mzXML file) from the pep.xml file. After sticking to > the convention listed above, assuming you still get failure in the > tools, what are the values of the two "base_name" attributes in the > pep.xml file? > > Did you start with an mzXML file to generate the mgf file using > MzXML2Search? If not, I don't believe you'll be able to run XPRESS as > the resulting .dat file (and converted pep.xml file) won't have the > scan number encodings in the convention that the TPP tools (such as > XPRESS) requires in order to properly access the spectral data. > > - Jimmy > > On Mon, Jun 28, 2010 at 4:42 PM, Brian Pratt <[email protected]> > wrote: >> Try renaming the mzXMl file to "F030382.mzXML", maybe? >> >> On Mon, Jun 28, 2010 at 4:37 PM, Jing Wang <[email protected]> wrote: >>> >>> 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. >> >> -- >> 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. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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