Downloading and using the software is free of charge.
The latest versions are
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.
Unpack the compressed folder, MaxQuant…zip, Perseus…zip or Andromeda…zip:
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.
MaxQuant/bin/conf/contaminants.fasta. It can also be downloaded separately from the MaxQuant download page, or directly from this link.
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.