There is a dizzying array of formats commonly used in MS-based proteomics , but the TPP tools primarily use three: mzML, pepXML, and protXML. The first step is often to convert the raw vendor format to mzML. The TPP distributions have bundled the ProteoWizard 10 msconvert tool for many years to provide this functionality, although a substantial drawback is that msconvert can only perform vendor-format conversion when running on the Windows platform, which complicates pipeline analyses on Linux and other platforms.