ms2mz is a free, simple utility for converting between common mass spectrometer file formats. The most common use of ms2mz is to convert proprietary vendor binary files (for example, Thermo RAW) to the standard MGF peak list format used for input to most proteomic search algorithms. We use ms2mz to prepare our files for upload to Proteome Cluster.
Download the exectuable here.
ms2mz is a simple GUI overlaying msconvert, part of the ProteoWizard suite of proteomics data tools. ProteoWizard supplies a msconvertGUI with the distribution which is adequate for most purposes. We use ms2mz because it offers better filter support, better support for the MGF title line “titleMaker” filter, support for merging files and support for saving conversion profiles. The ability to save conversion profiles helps to make sure that the same conversion parameters are used for the same experiment types and allows researchers to share conversion profiles, encouraging reproducbile data analysis. For example, we commonly use two conversion profiles. One converts binaries to mz5. The other converts binaries or open raw file formats (mzML, mzXML, mz5) to MGF format, keeping the top 100 MS/MS peaks and inserting a descriptive MGF title line.