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Download and Installation Guide

The latest MaxQuant release is:


Downloading and using the software is free of charge, but you must register first. You will receive an email with a registration code that you can use any time you want to download a new version. If you already have a registration code, you can skip Step 1.

  1. First time users should go to the registration page of MaxQuant. The Viewer and Andromeda are packaged with MaxQuant, but in case you want to use Andromeda's stand-alone version you can register here.
    1. Fill out the Registration form.
    2. Press “Submit”.
  2. You will soon receive an E-Mail with the URL for downloading the software and a personal registration code.
    1. Open the download page of MaxQuant or Andromeda's stand alone version in your browser.
    2. In the text box, enter your registration code.
    3. Press “Submit”.
  3. You will be forwarded to the webpage where you can download the latest version to your computer.
  4. Unpack the compressed file


Please choose your operating system to view how to run MaxQuant.

MaxQuant on Windows
Supported operation system versions (64 bit is required) are Windows Vista, 7, 8, 10, Server 2008, 2012.

Double click on MaxQuant.exe in MaxQuant folder and specify your RAW files, experimental design and fasta files.

  • Start MaxQuant

Click on the Start button.

MaxQuant on Linux
We are supporting and testing MaxQuant on Ubuntu 16.04.3 or higher, but MaxQuant should also work on another distribution of Linux.
You may run MaxQuant using Graphical User Interface. In this case, you should install Mono and follow instructions for MaxQuant on Windows starting from second point. This tutorial is focused on running MaxQuant using command line.
  • Install Mono Framework 5.4.1 or higher

To find out whether you already have it, type in the command line

mono --version

If you need to, you can download the software and get installation instructions at the Mono Download page.

  • Edit mqpar.xml file

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.

  • Run MaxQuant
mono MaxQuant/bin/MaxQuantCmd.exe mqpar.xml

Hardware requirements

  • Intel Pentium III/800 MHz or higher (or compatible) although one should probably not go below a dual core processor.
  • 2 GB RAM minimum.
  • 2 GB RAM per thread that is executed in parallel is required.
  • There is no upper limit on the number of cores. Whatever you can fit into a shared memory machine will work as long as the disk performance scales up with it.
maxquant/common/download_and_installation.1527600007.txt.gz · Last modified: 2018/05/29 15:20 by sinitcyn