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ProteoWizard / pwiz

The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
http://proteowizard.sourceforge.net/
Apache License 2.0
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Issues converting Waters raw to mzML #1922

Closed jonaheaton closed 11 months ago

jonaheaton commented 2 years ago

I'm am trying to convert Waters raw data originating from a XEVO-G2XSQTOF machine to an mzML format. When I use the msconvert windows GUI app, it crashes without any error message at all, and using the command line I get the following message: "caught unknown exception" please report this error

I am using the vendor peak picking ("peakPicking true 1-") and looking in the raw data folder, I do see that a centroid.raw file is created and there are data files inside with what I suspect is the properly centroided data. However MSconvert appears to run into an error before this data is written to mzML file. command_output.txt I don't think I am the first one with this issue: Example 1: https://github.com/ProteoWizard/pwiz/issues/775 Example 2: https://sourceforge.net/p/proteowizard/mailman/message/36714564/

Both the "_HEADER.TXT" and the "_extern.inf " have three functions, although there appears to be .DAT and .IDX files for a 4th function in the raw data. Deleting those files associated with the 4th function doesn't help.

Thanks for any help you can give! Best, Jonah

chambm commented 11 months ago

The set mass won't work yet with lockmass correction. That's going to be fixed by #2770 .

chambm commented 11 months ago

OK, you should now be able to get lockmass corrected precursor mass either with or without DDA processing mode. That fix and the others Pete mentioned are available in the current ProteoWizard download.