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 -~----------~----~----~----~------~----~------~--~---
