Maxquant

Introduction

Maxquant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.

For more information, please check home page: https://www.maxquant.org.

Versions

  • 2.1.0.0

  • 2.1.3.0

  • 2.1.4.0

  • 2.3.1.0

Commands

  • MaxQuantGui.exe

  • MaxQuantCmd.exe

Module

You can load the modules by:

module load biocontainers
module load maxquant

GUI

To run Maxquant with GUI, it is recommended to run within ThinLinc:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers maxquant
(base) UserID@bell-a008:~ $ MaxQuantGui.exe
../../_images/maxquant.png

CMD job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Maxquant without GUI on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=maxquant
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers maxquant

MaxQuantCmd.exe mqpar.xml