MaxQuant for Linux Guide
Read my blog post here: http://atchen.me/research/2019/03/21/mq-linux.html
The goal of the
gen_mqpar.py script is to create MaxQuant configuration files (
mqpar.xml files) in a console environment without having to transfer one over or edit the XML manually. The example given has some hard-coded stuff and makes assumptions about your filesystem, so please follow the steps below to get started.
- Verify that Mono is installed.
Note, If searching Bruker timsTOF data, you need
gcc version 8.3+. Check the version with
gcc --version. You can install gcc8 with these commands:
# For CentOS 7: yum install centos-release-scl yum install devtoolset-8 scl enable devtoolset-8 -- bash # Enable the tools (put this into .bash_profile) source /opt/rh/devtoolset-8/enable
- Create template
mqpar.xmlfiles – representing configurations for MaxQuant searches you routinely run on your experiments. I put a bunch of my templates in a folder,
templates/for easy access.
- I recommend generating these first in the MaxQuant GUI, as it's easier and you can verify that the configuration file is valid before moving it to your Linux instance.
- Don't worry about the raw files, folder paths, or FASTA file paths in the template file – they will be replaced by the script
- Move the MaxQuant files onto your Linux instance. My setup has MaxQuant versions separately in a folder
MQ/MaxQuant_1_7_0. I then map this path to an environment variable in my
export MQ_1_7_0=~/MQ_1_7_0/bin/MaxQuantCmd.exe. You can manage your MaxQuant versions however you like, just make sure that it's reflected in the
- Move your protein FASTA files over to the Linux instance. The current
gen_mqpar.pyscript has the path to the FASTA file hard-coded, and it's straightforward to change this or make it argument-driven.
./gen_mqpar.py <path/to/template> <path/to/raw_file_folder> -o <path/to/output_mqpar.xml> -t <num_threads> # for example, ./gen_mqpar.py templates/SILAC.xml raw_files/FP93 -o fp93_silac.xml -t 6
If you're getting errors with starting MaxQuant with the generated
mqpar files, then I would manually check all of the paths in the XML file first.