From the MaxQuant home page: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. The search engine andromeda is integrated into MaxQuant as well as the viewer application for inspection of raw data and identification and quantification results.



Authorized Users

  • CIRCE account holders
  • SC account holders


  • CIRCE cluster
  • SC cluster


MaxQuant requires the following module file to run:

  • apps/maxquant/

Running MaxQuant on CIRCE/SC

The MaxQuant user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Interactive Mode

To run MaxQuant in an interactive session using the graphical interface, use srun to enter an interactive shell. This example is for 30 minutes using 1 cpu core:

[user@itn0 ~]$ srun --time=00:30:00 --ntasks=1 --pty /bin/bash

Once you get dropped into an interactive shell on the execution host, you need to load the MaxQuant module.

[user@svc-3024-22-7 ~]$ module load apps/maxquant/

You should now be able to execute the GUI version (interactive mode) from the command line.

[user@svc-3024-22-7 ~]$ mono $MQHOME/bin/MaxQuantGui.exe

Submitting a Job

Use a submit script like the following to run MaxQuant:

#SBATCH --job-name=maxquant-test
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --mem-per-cpu=2048
#SBATCH --output=output.%j.maxquant-test
#SBATCH --time=01:00:00

#### SLURM single node test 
#### to run for 1 hour 
#### using 4 processor cores and 8 GB of memory

module purge
module add apps/maxquant/

mono $MQHOME/bin/MaxQuantCmd.exe filename.xml


Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./
  • You can view the status of your job with the “squeue -u <username>” command


Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with MaxQuant to the IT Help Desk: