It's assumed you (or someone in your group) can build Mascot2XML since we don't provide linux binaries, so it's just a matter of getting updated code and doing another "make all install".
One way to do that is to just to run "wget https://sashimi.svn.sourceforge.net/svnroot/sashimi/trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Mascot2XML/MascotConverter.cxx " then copy *MascotConverter.cxx * over the old file and rebuild. - Brian On Fri, Sep 18, 2009 at 12:59 AM, lgillet <[email protected]> wrote: > > 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. 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