This is an old revision of the document!
The latest MaxQuant release is: 220.127.116.11
Downloading and using the software is free of charge.
Simply download from here and unpack the compressed file MaxQuant.zip.
Please choose your operating system to view how to run MaxQuant.
Double click on MaxQuant.exe in MaxQuant folder and specify your RAW files, experimental design and fasta files.
Click on the Start button.
To find out whether you already have it, type in the command line
If you need to, you can download the software and get installation instructions at the Mono Download page.
Currently we highly recommend to preconfigure the mqpar.xml file in MaxQuant GUI. After transferring the file on Linux machine, do not forget to update file addresses accordingly.
mono MaxQuant/bin/MaxQuantCmd.exe mqpar.xml