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MaxQuant (using mqpar.xml) (version
Specify one or more Thermo RAW files
Specify one or more FASTA databases.
Modify parse rules if needed

MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.

This tool is a wrapper for MaxQuant v2.0.3.0. It gets its search parameters from a previously created parameter file (mqpar.xml). A similiar tool that allows the specification of search parameters directly through galaxy is available as well and should be preferred, if possible.

Input files

Output files

Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented.