Convert mass spectrometry data file formats with msconvert

By bgruening

March 24, 2019

msconvert is a tool to convert mass spectrometry data file formats.

A list of supported file formats is given below:

agilentbrukeryep.d.tar
agilentmasshunter.d.tar
brukerbaf.d.tar
brukertdf.d.tar
watersmasslynx.raw.tar
thermo.raw
wiff
wiff.tar
mzml
mzxml
mz5
mgf
ms2

This tool is special in multiple ways. At first its one of the few tools that only runs in a very special Container, created by Dr. Matt Chambers, including Wine and Proteowizard. This is because many of the underlying libraries do need a Windows runtime environment and Matt found a way to make this available in a Container so Galaxy Europe and all others can use it on there Cloud systems.

Because msconvert is part of Proteowizard you need to agree with the vendor licenses before you can use this tool.