Skip to content

MaxQuant

Cox, J. and Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol, 2008, 26, pp 1367-72. Note that the paper has a large supplement containing in-depth descriptions of algorithms.

MaxQuant is a proteomics platform for peptide identification, quantification, and downstream analysis of large mass-spectrometry datasets. LAMPrEY uses it to process individual Thermo Fisher .raw files inside a reproducible pipeline workflow.

The software supports label-free and isobaric workflows, and LAMPrEY extracts a standard quality-control table from the generated summary.txt, proteinGroups.txt, peptides.txt, msmsScans.txt, and evidence.txt outputs.

The QC layer currently captures metrics such as:

  • acquisition summary values from summary.txt
  • protein-group counts, contaminant counts, sequence coverage, and per-channel TMT missing values
  • peptide counts, oxidation rates, and missed-cleavage distributions
  • precursor and calibration metrics from msmsScans.txt and evidence.txt
  • QC peptide and QC protein reporter-intensity summaries when the expected targets are present

To generate an input parameter file for LAMPrEY, create the configuration in a local MaxQuant installation with a single representative RAW file, then export the resulting mqpar.xml and upload it to the server as part of a pipeline setup.

Runtime selection is version-aware:

  • MaxQuant versions earlier than 2.6 run through mono
  • MaxQuant versions 2.6 and newer run through dotnet
  • the runtime is selected automatically from the uploaded binary, but can be overridden with MAXQUANT_RUNTIME=mono or MAXQUANT_RUNTIME=dotnet

The repository also includes a bundled MaxQuant executable ZIP under app/seed/defaults/maxquant/. That asset is stored with Git LFS, so contributors and operators should install git-lfs before cloning the repository.