MaxQuant

Software Summary

Mesabi

Default Module:

Other Modules Available:

Last Updated On:

Mesabi K40

Default Module:

Other Modules Available:

Last Updated On:

Mangi

Default Module:

Other Modules Available:

Last Updated On:

Mangi v100

Default Module:

Other Modules Available:

Last Updated On:

NICE

Default Module:

Other Versions Available:

Last Updated On:

Tuesday, June 24, 2014

Support Level:

Secondary Support

Software Access Level:

Open Access

Home Page:

Link

Software Categories:

Proteomics

Software Description

MaxQuant is a quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets.

Software Documentation

Software Documentation Tabs

General Linux

Currently MQ in Linux works only from the command line; the GUI is not currently working. Mono is required in order to run it. The process for running on Linux is as follows:

1. Download a version of MaxQuant that is compatible with Linux (>= v1.6.1.0) and copy it to your MSI home directory.

2. In Windows, set up your MaxQuant jobs and parameters completely. Specify your input (raw) files, your search database, PTMs, thread count, etc. Do everything except hit run.

3. In Windows, go to File -> Save Parameters. Specify a file name and location for the xml file. If you're running it on Citrix make sure to save it to your own directory (rather than a volume local to Citrix) so you can easily pull it up on Mesabi or Itasca.

4. In Linux, edit the parameters file to denote the file locations for your search database and raw files. You may want to then save it under a different name.

5. In Linux, use the command "module load mono" to load mono

6. In Linux, use the command "mono MaxQuantCmd.exe my_mq_params.xml" where "my_mq_params.xml" is the file edited in 3. You'll likely need to specify the full path for "MaxQauntCmd.exe" as well; it is in your MaxQuant directory under "MaxQuant/bin"

A couple notes:

1. The version you use to create the xml configuration file in Windows must *exactly* match the version you are running in Linux. Configuration files that correspond to mismatched MQ versions will cause MQ to crash in most cases.

2. In most cases the jobs will need to be submitted to a job queue.

The official documentation can be found here.