It would be interesting to see the difference between the mzXML file that worked and the one that didn't.
X!Tandem has its own mzXML parser and it might need a tweak. Perhaps you could send me those files? Thanks, Brian -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Oded Sent: Saturday, August 15, 2009 1:08 PM To: spctools-discuss Subject: [spctools-discuss] RAW to mzXML (and mzXL) problem TPP4.3 Hi, I'm having problems converting RAW data to mzXML with TPP4.3. I tested different files on 2 different WinXP computers installed with TPP4.3. The conversion to mzXML goes just fine and the output can be used with Pep3D. However, while trying to run a Tandem search with the TPP4.3-generated mzXML file as input the following error message pop-up: run_in.exe error run_in.exe has encountered a problem and needs to close. We are sorry for the inconvenience. In the detailes section I can see that the error signature is: szAppName : run_in.exe szAppVer : 0.0.0.0 szModName : msvcrt.dll szModVer : 7.0.2600.5512 offset : 00037b26 If I try to use the same mzXML for X! Tandem search on a Mac running TPP 4.3 (or 4.2) I'm getting the following message: X! TANDEM 2 (2007.07.01.3) Loading spectra .Unsupported compression type 'none'. Command FAILED I tried to use different conversion options (i.e profile, centroid, with or with out comprssing) but still got the same error messages. In addition conversion to mzXL failed showing the following error message c:\Inetpub\tpp-bin\msconvert -v --mzML -o c:/Inetpub/wwwroot/ISB/data/ Test/Markers -c [1,2] c:/Inetpub/wwwroot/ISB/data/Test/Markers/ LFok08.RAW Unable to read configuration file [1,2] format: mzML (Precision_64 [ 1000514:Precision_64 1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None) indexed="true" outputPath: c:/Inetpub/wwwroot/ISB/data/Test/Markers extension: .mzML contactFilename: filters: filenames: c:/Inetpub/wwwroot/ISB/data/Test/Markers/LFok08.RAW processing file: c:/Inetpub/wwwroot/ISB/data/Test/Markers/LFok08.RAW [MSDataFile::readFile()] Unsupported file format. Error processing file c:/Inetpub/wwwroot/ISB/data/Test/Markers/ LFok08.RAW Converting the same files on TPP4.2 (rev1) generate fully "fuctional" mzXML files. Any help would be appreciated, Oded --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
