Hi David, I think there's a way to overcome this Mascot mzXML problem. It's slightly more troublesome, but with no other alternatives, I think it's still manageable.
This is what I did: vendor's format -> mzXML -> mgf -> Mascot search output -> place these output files together with mzXML files (but renamed as the corresponding Mascot output filenames just before the .mzXML extension) It worked for all 16 files except for 1 which gave the following error msg: variable modification 5, delta mass 15.9949 for Oxidation (M): residues: M nterm: 0 cterm: 0 protterm: 0 Assertion failed: masses->length() == intens->length(), file Parsers/ Algorithm2XML/Mascot2XML/MascotConverter.cxx, line 2079 This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. command "C:\Inetpub\tpp-bin\Mascot2XML.exe c:/Inetpub/wwwroot/ISB/data/ Proteominer/Cartridge1Solv1/RNP00186S00209FR12.d.mgf_F060145.dat -Dc:/ Inetpub/wwwroot/ISB/data/dbase/ipi.RAT.v3.49.fasta -Etrypsin -desc - shortid" failed: No such process END OUTPUT RETURN CODE:768 ###### End Command Execution ###### # All finished at Wed Jun 10 17:26:44 2009 # END COMMAND BLOCK Do you have any idea what's the issue here? Or who should I look for to help solve this Mascot2XML converter problem? Thanks, Bernard --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
