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 see the version 2.1.811, then everything is ready to start MaxQuant.
Overwise you need to get installation instructions at the .NET Core SDK 2.1.811 for your operation system.
wget https://packages.microsoft.com/config/ubuntu/20.04/packages-microsoft-prod.deb -O packages-microsoft-prod.deb sudo dpkg -i packages-microsoft-prod.deb sudo apt-get update; \ sudo apt-get install -y apt-transport-https && \ sudo apt-get update && \ sudo apt-get install -y dotnet-sdk-2.1
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. You can also use a programmatic way to change that.
dotnet MaxQuant/bin/MaxQuantCmd.exe --changeFolder=new_mqpar.xml <new folder with fasta files> <new folder with raw files> old_mqpar.xml
However if you feel familiar with a structure of mqpar.xml, you may create a template of mqpar.xml and edit it directly.
dotnet MaxQuant/bin/MaxQuantCmd.exe --create new_mqpar.xml
dotnet MaxQuant/bin/MaxQuantCmd.exe mqpar.xml