MaxQuant is a software package for mass spectroscopy and proteomics. There is a windows version and a linux version. To run on linux you have to use a program that is called mono. I think, it is developed by Microsoft, which I find quite nice from them. I installed mono on Linux and started MaxQuant.

mono MaxQuant.exe

The documentation claims it is for running MaxQuant in commandline mode, though a GUI is started anyway. How can I start the program in commandline mode to perform batch analysis? I think, there is not enough information given on the web-page.


2 Answers 2



mono MaxQuantCmd.exe [OPTIONS]

a try.

University of Oslo description of how to use the tool in their infrastructure.

  • $\begingroup$ Kohl, the link is broken. Could you update it please? $\endgroup$
    – Gian Arauz
    Commented Jul 14, 2022 at 12:30

You can now install MaxQuant simply with Conda:

conda install -c bioconda maxquant

and to run MaxQuant type:

maxquant mqpar.xml



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