ProteoWizard HowTo

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ProteoWizard is a de facto standard tool to convert various mass spec file format. See wikipedia for more details about mass spec data format.

After 2013, mzML becomes the standard format for mass spectrometry proteomics data format. Before then, mzXML was widely used standard format. However, both formats are based on XML, so it is not human-readable format.

If you want to inspect your MS data in text format, I recommend to use MS1/MS2 format. See ms2 format description and the paper for more details.

Batch Script

Type the following line to make 'convert.bat', and run it on Windows Command (See ref how to launch command prompt).

"c:\Program Files\ProteoWizard\ProteoWizard 3.0.9870\msconvert.exe" --32 --mzXML --gzip *raw

I used 32-bit encoding for spectrum (--32) and made mzXML (--mzXML), instead of mzML, for compatibility to old search engines. Also, to save the storage space, I compressed the output with gzip (--gzip). You can turn it off these options if you want.