Mascot2XML is often problematic, since it tries to figure out scan descriptions from a variety of formats that have then been passed through Mascot - it's an ever shifting landscape. It appears you've hit on a new variant. If you want to send me a small sample I can see about tweaking the code (ftp://insilicos.serveftp.net/pub).
I agree that reading the Mascot pepXML directly would be ideal, perhaps you could give an example of that as well and we can see if it's close to being useful or not. Brian Pratt Insilicos On Thu, Sep 10, 2009 at 8:38 AM, lgillet <[email protected]> wrote: > > Hi, > > I am running into troubles with the Mascot2XML command on the TPP. > I followed the steps specified in the TPP wiki: > basically file.mzXML => file.mgf conversion => Mascot searching => > Fxxx.dat => renamed file.dat > I copy the file.dat where the original mzXML is, and with the > database. I run the command: > Mascot2XML file.dat -D./database.fasta > > Here start the troubles: I get tons of warnings like: > > "Warning: could not find scan numbers of spectrum > spectrumId=3974Polarity=PositiveScanMode=MassScanTimeInSeconds=3916.82 > Set to 0000" > > (though again, the mzXML file with the same name is in the very same > directory). > But ok... > > Now the last error is more puzzling: > > " 998. opening > Thu_Sep_10_17-19-28_2009.spectrum937.0000.0000.4.out > econds=1745.3.out > error: only found 1 periods in > spectrumId=1472Polarity=PositiveScanMode=MassScanTimeInSeconds=1428.2 > " > > And then, when I look into the created file.pep.xml, the file seems > truncated at the end: > > " <spectrum_query > > spectrum="spectrumId=1472Polarity=PositiveScanMode=MassScanTimeInSeconds=1428.2" > > No ending like in regular .pep.xml files as it should ( > "</spectrum_query> > </msms_run_summary> > </msms_pipeline_analysis>" > at least!!) > > Of course, no chance to start an xinteract on that truncated > file.pep.xml > > So do I do anything wrong? I could not process mascot .dat files > neither from an old 2.1 nor from a newer 2.2.06. For both of those, > the .dat files gave the same problems. Also this error is reproducible > on TPP 4.0 and the latest release I could test. > > Do you have any idea how to help this out? > > Finally, maybe a very stupid question, but Mascot is also able to > export results in the pepXML format. But the resulting file is not > processed by xinteract. That's a pity because that would be a serious > shortcut instead of running into the "Mascot2XML" business. Any idea > why xinteract cannot process the Mascot's pepxml files? > > Thanks in advance for you feedbacks. > > Ludovic > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
