Hi Brian, Thanks for your reply. I also figured out the variant of the "title" string. I think this depends on the file type searched (mgf or mzdata) and the version of Mascot as well. Thanks for having fixed that. I am no informatician and I am not sure I understand how I should proceed to get the fix: you mention to rebuild Mascot2XML from the trunc, and I guess you cannot send me the Mascot2Xml executable that you built on your system (since I imagine it might not be compatible with the TPP we built here on our Unix system), am I right? Where could I then find this fixed version of the "trunc"? Is this in a "nightly built" of TPP or something like this? Do you plan to release the fixed Mascot2XML in the next complete TPP version? Also, I will give a try to contact the Mascot team to ask if they can fix their pepxml export issue. That would be nice for all people using Mascot and TPP in the future.
Anyway, thanks a lot again for your help, Best, Ludovic On Sep 11, 8:37 pm, Brian Pratt <[email protected]> wrote: > 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 -~----------~----~----~----~------~----~------~--~---
