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.

References:

• Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008 Dec;26(12):1367-72.
• Tyanova S, Temu T, Cox J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc. 2016 Dec;11(12):2301-2319.

• MaxQuant Main Site

• Module Name: maxquant (see the modules page for more information)
• Multithreaded
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.

This application requires a graphical connection.

The most recent versions of MaxQuant do not fully support the graphical interface on Linux.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load maxquant
[user@cn3144 ~]$ MaxQuantGui.exe

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

An interactive window will pop up: