Actually, after a discussion on the phone with Jimmy, I think that the -c1-3 option is not needed in this case and will cause some extra searches being run. Just use
MzXML2Search -mgf *.mzXML And then rename the resulting .dat file to match the input basename. -David On Mon, Jun 28, 2010 at 5:24 PM, David Shteynberg <dshteynb...@systemsbiology.org> wrote: > 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 <jke...@gmail.com> 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 <brian.pr...@insilicos.com> >> wrote: >>> Try renaming the mzXMl file to "F030382.mzXML", maybe? >>> >>> On Mon, Jun 28, 2010 at 4:37 PM, Jing Wang <fayfay9...@gmail.com> 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 <brian.pr...@insilicos.com> >>>> 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 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. >>> >> >> -- >> 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. 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