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MaxQuant

MaxQuant

Description

MaxQuant: MaxQuant is a quantitative proteomics software package designed for analyzing large massspectrometric data sets. You can read documentation about the software here

 


Available

Version on CSC's Servers

mono/5.16.0.179 (Installed on Taito)

MaxQuant (>= v1.6.1.0) (Register and download MaxQuant software; use the same version of MaxQuant both on linux and windows)


Usage

  • Download Linux-compatible version of MaxQuant (>= v1.6.1.0)
  •  In Windows, set up the parameters of MaxQuant  including specifying  input (raw) files, your search database, PTMs, thread count, etc.  Do not run analysis.
  • In Windows, go to File -> Save Parameters file as .xml file  
  • In Linux, edit the parameters file to denote the file locations for your search database and raw files.
  •  In Linux, use the command "module load mono" to load mono
  •  Run  "mono MaxQuant/bin/MaxQuantCmd.exe mqpar.xml"

 

Typical batch script would look like this:

#!/bin/bash

#SBATCH -J maxquant

#SBATCH -o output_%j.txt

#SBATCH -e errors_%j.txt

#SBATCH -t 01:20:00

#SBATCH -n 1

#SBATCH -p serial

#SBATCH --cpus-per-task=12

#SBATCH --mem=16000


#set up commands

module load mono

#run the command

mono /path/for/MaxQuant/bin/MaxQuantCmd.exe /path/for/mqpar.xml


Discipline

Biosciences

References

P Sinitcyn, S Tiwary, J Rudolph, P Gutenbrunner, C Wichmann, Ş Yılmaz,  MaxQuant goes Linux; ; Nature methods 15 (6), 401


Support


Manual