Hi SKV, thank you for your note. I don’t really know what the problem might be based on your description. As you surmise, there can be problems when files exceed a 2 GB or 4GB limit on some systems, I am forwarding your message to the spctools-discuss list, because here there are gurus who can better answer your question. I think they will need to know what type of computer & operating system you’re running on. Is it Windows or Linux? Is it 32-bit or 64-bit? Also, can you say which version of the TPP you’re using.
Is there a wiki page on what’s known to work and not work wrt large files? With this information, hopefully someone can say how to fix your problem. You might consider using mzML instead of mzXML, although that may not solve your problem. Regards, Eric *From:* Adhin, S.K.V. [mailto:[email protected]] *Sent:* Monday, January 28, 2013 4:12 PM *To:* [email protected] *Cc:* [email protected] *Subject:* TPP / X!Tandem error Dear Mr. Deutsch I am a master student at the Free University Amsterdam, the Netherlands. Last autumn I visited your talk about the different file formats used for mass spectrometry data and the Trans-Proteomic Pipeline. Actually nowadays I am using this tool for my master graduation project. I succesfully manage to use the TPP for many mass spectrometry files. I always used MSConvert to convert the .raw files to the mzXML file format. Unfortunately the new files from qe-jurkat can not be parsed correctly when I do the database search in the TPP (by using X!Tandem). The error message that I get is: * * *X! TANDEM CYCLONE TPP (2011.12.01.1 - LabKey, Insilicos, ISB) * * * *Loading spectra (mzParser)............ loaded.* *Spectra matching criteria = 22587* *Pluggable scoring enabled.* *Starting threads .* *This application has requested the Runtime to terminate it in an unusual way.* *Please contact the application's support team for more information.* I tried to index the mzXML file again, but that did not help. I also read something about the charge state, so I did put that to zero, still I get the same error message. The only thing I can think of is that the mzXML I am working with now are significantly larger (5.5 - 6.0 GB) than the ones I used before. Could that be a reason that a database search can not be done on these files? Any kind of help would be very much appreciated. Sincerly yours, S.K.V. Adhin, BSc -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
