mzML and mzXML file support

May 5, 2011

Proteome Cluster now supports uploads of mzML and mzXML files in addition to MGF files. mzML and mzXML files are converted on-the-fly to MGF format for searching.

mzML and mzXML files preserve both MS1 and MS2 data, while MGF files only contain MS2 data. As a result mzML and mzXML files are larger than MGF files derived from the same source file. But they can be used to derive peak areas and intensities for quantitation purposes.

We are simultaneously releasing our free ms2mz application for converting from mass spectrometry vendor binaries to mzML, mzXML or MGF. Learn more about it and download it here.

Both Proteome Cluster and ms2mz rely on msconvert, part of the excellent ProteoWizard toolbox.

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