Hi Ludovic, I got the files, thanks. As I expected, it's yet another variant of the "title=" string, and pretty simple to correct (rebuild Mascot2XML from the trunk source to get the fix).
The issue with the pepXML as written by mascot is that it's simply incomplete - the scan number and retention time info are written properly. For example: <spectrum_query spectrum="spectrumId=3788 Polarity=Positive ScanMode=MassScan TimeInSeconds=3725.23" *start_scan="0" end_scan="0"*precursor_neutral_mass="592.472752" assumed_charge="2" index="4"/> should be <spectrum_query spectrum="spectrumId=3788 Polarity=Positive ScanMode=MassScan TimeInSeconds=3725.23" *start_scan="3788" end_scan="3788"* precursor_neutral_mass="592.472752" assumed_charge="2" index="4" * retention_time_sec="3725.23"/*> but obviously you'd have to take that up with the folks at Matrix Science. They are trivially close to being correct, hopefully they can fix that for you. - Brian On Thu, Sep 10, 2009 at 10:42 AM, Brian Pratt <[email protected]>wrote: > 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 -~----------~----~----~----~------~----~------~--~---
