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Download and Installation Guide

Downloading and using the software is free of charge.

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.

Software requirements

Concerning all software

  • Supported OS versions are
    • Windows Vista SP2 (x64)
    • Windows 7 SP1 (x64)
    • Windows Server 2008 R2 SP1 (x64)
    • Windows Server 2008 SP2 (x64)
    • Windows 8
    • Windows 10
    • Windows Server 2012
  • 64 bit is required.
  • .NET Framework 4.5 or higher from Microsoft. Follow the link for installation instructions and version information.


The latest versions are

  • MaxQuant
  • Perseus
  • Andromeda

Bug fixes, changes, and new features can be reviewed on these pages, which are also available with the releases as bin\

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 or Perseus. 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, Perseus 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.


Unpack the compressed folder, MaxQuant…zip, Perseus…zip or Andromeda…zip:

  1. An appropriate program for compressed file has to be installed on your computer. For example, many users use WinZip, WinRAR or Pkzip to extract .ZIP files
  2. Locate the compressed folder that you want to extract files or folders from.
  3. Right-click the folder, click Extract All, and then follow the instructions.

That's it! To start MaxQuant, Perseus or Andromeda's standalone-version, simply open the decompressed folder and click on the executable - “MaxQuant.exe”, “Perseus.exe” or “Andromeda.exe”.

Normally you will want to run MaxQuant through the GUI, but in the bin folder there is also a command line version, MaxQuantCmd.exe, that requires an mqpar.xml file as the sole argument.

File downloads

  • MaxQuant
    • The contaminants file can be found in any MaxQuant installation under
      MaxQuant/bin/conf/contaminants.fasta. It can also be downloaded separately from the MaxQuant download page, or directly from this link.
  • Perseus
    • The annotations file can be downloaded from within the Perseus software or obtained here.

.NET Framework 4.5

You will need .NET Framework 4.5 or higher to run MaxQuant. (The latest version, 4.6.2, was released on 2016-07-20.) To find out whether you already have it, follow the instructions on How to Determine Which .NET Framework Versions Are Installed. If you need to, you can download the software and get installation instructions at the Microsoft Download Center.


MSFileReader is the standard library used by MaxQuant to access raw Thermo files.

  1. Go to to register with Thermo and be able to download MSFileReader 3.0. If you have registered before, you can go directly to to login.
  2. Once you are registered and logged in, you can download MSFileReader 3.0 from the Thermo web site. It is currently under “Utility Software”. The latest version (as of 2017-02-09) is
    MS File Reader 3.1 SP4,
    available since Feb 21, 2017. MaxQuant has been most thoroughly tested with MS File Reader 3.0 SP2.
  3. Unzip it
  4. Right click on the installer and “Run as Administrator”
  5. Install it accepting defaults
  6. If given the option, install both 32-bit and 64-bit versions.
maxquant/common/download_and_installation.txt · Last modified: 2015/11/23 14:36 (external edit)