MaxQuant

Published

May 13, 2025

Modified

May 13, 2025

Starting a run with the GUI

  1. Specify raw data

    • fill in Experiment or set No fractions

  2. Group specific parameters:

    • for LFQ:
      • Type: Standard, Multiplicity: 1
      • Label-free quantification: LFQ
      • Digestion

  3. Global parameters:

    • Fasta file: Proteome from Uniprot
    • Tables: mzTab

Updating the xml file generated above

  1. dotnet MaxQuant xml-from-the-previous-run --changeFolder new-xml fasta-file raw-data-path
Terminal
.../dotnet .../MaxQuant/bin/MaxQuantCmd.dll mqpar.xml --changeFolder mqpar-modified.xml . .
  1. Set number of cores

<numThreads>4</numThreads>

  1. Starting a run on the server
Terminal
nohup .../dotnet .../MaxQuant/bin/MaxQuantCmd.dll mqpar-modified.xml > nohup.out 2> nohup.err