How to run MaxQuant in command line mode? 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.
Give 

mono MaxQuantCmd.exe [OPTIONS]


a try.

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