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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.

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Give

mono MaxQuantCmd.exe [OPTIONS]

a try.

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

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You can now install MaxQuant (v. 1.6.10.43) with anaconda:

conda install -c bioconda maxquant

and to run MaxQuant simply with:

maxquant.sh mqpar.xml

Reference

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