Thermo Xcalibur RAW data to MGF
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hwu12 ▴ 10
@hwu12-12353
Last seen 5 weeks ago
United States

I was wondering if there is any bioconductor package can convert the RAW file from Thermo Xcalibur to MGF file? If not, is there anything available for Mac OS? Thanks!

mass spectrometry massspectrometry • 1.6k views
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@laurent-gatto-5645
Last seen 4 days ago
Belgium

The short answer is no, because to access (and this convert) proprietary Thermo raw data, you need to their libraries that are only available on Windows. That would mean that an R package would need to (i) incorporate these proprietary binary Thermo libraries and (ii) only be available on Windows.

You will need to use msconvert from the Proteowizard project (on Windows) to convert them to an open format such as mzML or mgf. The latter can be processed in R with MSnbase.

It is apparently possible (although I have never tried it myself) to get the Thermo libraries to run under Mono on Linux. I don't know if this would also work on OSX though.