How to run MaxQuant in command line mode?

Question

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.

score 2 · Accepted Answer · answered Jul 13 '18 at 22:21

2

Give

mono MaxQuantCmd.exe [OPTIONS]

a try.

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

answered Jul 13 '18 at 22:21

Kohl Kinning

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Kohl, the link is broken. Could you update it please? – Gian Arauz Jul 14 '22 at 12:30

Soerendip · Answer 2 · 2022-05-18T00:58:20.340

0

You can now install MaxQuant simply with Conda:

conda install -c bioconda maxquant

and to run MaxQuant type:

maxquant mqpar.xml

Reference

edited May 18 '22 at 00:58

answered Jul 21 '20 at 17:57

Soerendip

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How to run MaxQuant in command line mode?

2 Answers2