MaxQuant

Overview

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 labelling techniques as well as label-free quantification are supported. The Command Line version has been enabled on the CSF

Restrictions on use

MaxQuant is freely available under the Freeware licence. For details see the license file with cat $MAXQUANT_LICENSE

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run.
Load one of the following modulefiles:

module load apps/binapps/maxquant/2.4.3.0

Running the application

MaxQuant is built for the .NET framework and is executed on the CSF3 using dotnet You can invoke the command line program in a job script using the following

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript


module load apps/binapps/maxquant/2.4.3.0

maxquant [OPTIONS]

# or

# dotnet $MAXQUANTDIR/bin/MaxQuantCmd.exe  [OPTIONS]

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Updates

None.