Download & Installation


Cox Lab


November 15, 2023

1 Download

Downloading and using the software is free of charge.

Simply download from here and unpack the compressed file

2 Running

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

2.1 MaxQuant on Windows

Supported operation system versions (64 bit is required) are Windows 10 or 11 or Windows Server 2016, 2019, 2022.

We are currently working on making MaxQuant compatible with .Net 7. This will be bring further advantages to speed and stability of the tool.

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

  • Start MaxQuant Click on the Start button.

2.2 MaxQuant on Linux

We are supporting MaxQuant on Ubuntu 20.04 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 in Section 2.1 for MaxQuant on Windows starting from second point. This tutorial is focused on running MaxQuant using command line.

  • Install .NET Core 3.1 To find out whether you already have it, type in the command line
dotnet --version

If you see at least version \(3.1.100\), then everything is ready to start MaxQuant.

Otherwise you need to follow the installation instructions at .NET Core SDK 3.1 for your operating system.

Ubuntu 22.04 (for example)

wget -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
  • 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. 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
  • Run MaxQuant
dotnet MaxQuant/bin/MaxQuantCmd.exe mqpar.xml

3 Hardware requirements

  • 4 GB RAM minimum.
  • 4 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.

Here we list some example hardware configurations that we are using in the lab and that we are quite happy with. These are mere examples and there is no reason to prefer specific vendors or brands.

3.0.1 Dell PowerEdge R820 (Intel)

  • 4x Intel® Xeon® E5-4640 2.40GHz, 20M Cache, 8.0GT/s QPI, Turbo, 8C, 95W
  • 128GB Memory for 4CPU (16x8GB RDIMM, 1600 MHz, Standard Volt, Dual Rank, x4)
  • PERC H710p integrated RAID Controller, 1GB NV Cache
  • 6x 900GB, SAS 6Gbps, 2.5-in, 10K RPM Hard Drive (Hot Plug)
  • RAID-0
  • OS: Microsoft Windows Server 2012 Standard

3.0.2 Standard PC

  • Processor: Intel® Core i7-2600 Processor (8M Cache,3.40 GHz)
  • OS: English original Windows® 7 Professional(64-Bit)
  • RAM: 16GB (4X4GB) 1333 MHz DDR3 Non-ECC 489916 1 [370-20205] 3
  • Primary Hard Drive: 256GB SSD Solid State Drive
  • Additional Hard Drive: 2TB (7.2k rpm) Serial ATA II with NCQ and 16MB Data Burst Cache
  • Graphics card: 512MB AMD Radeon HD 6350
  • USB 3.0: USB 3.0 PCI-Card
  • To improve the processing speed the SSD can also be used exclusively for MaxQuant
  • USB 3.0 convenient for fast file transfer, 500MByte/s (USB 2.0 = 60MByte/s)
  • Hard drives can of course be larger depending on the respective sizes of your projects and wallet.

3.0.3 ‘Monster’ PC

  • Coolermaster HAF 922 Black Tower Case
  • 2 x Front USB 2.0 and Audio ports
  • 750W EPS12V Quiet power supply
  • Additional Red LED 200mm Case Fans
  • Asus Sabertooth P67 Intel i7 Skt1155ATX motherboard With 2 x 16x 2.0 PCI-Express slot, 3 x PCI-e x1 slot, SATAIII 4 x DDR3 memory slots, Audio, 10/100/1000 LAN, SATAII, & USB 3.0/USB 2.0 ports
  • Intel i7 2600K 3.4GHz Quad Core 8MB cache Skt1155 Unlocked processor
  • Corsair Vengeance 32GB (4 x 8GB) DDR3 1866MHz Quad Channel memory
  • Western Digital 500GB Caviar Black SATAIII disk drive
  • 1GB Nvidia Geforce GT430 PCI-e x16 2.0 graphics card
  • Black DVD+/- R RW Dual Layer drive
  • LSI 9260-8i 8port SAS 6Gb/s PCI-Express RAID controller
  • Battery Backup for RAID controller
  • 2 x Crucial 512MB Solid State Disks
  • Thanks to Peter McHardy for assembling this configuration

For question or problems with the installation we would love to hear from you under Contact.