nfcore/mhcquant is a bioinformatics analysis pipeline used for quantitative processing of data dependant (DDA) peptidomics data.

It was specifically designed to analyse immunopeptidomics data, which deals with the analysis of affinity purified, unspecifically cleaved peptides that have recently been discussed intensively in the context of cancer vaccines.

The workflow is based on the OpenMS C++ framework for computational mass spectrometry. RAW files (mzML) serve as inputs and a database search (Comet) is performed based on a given input protein database. FDR rescoring is applied using Percolator 3.0 based on a competitive target-decoy approach (reversed decoys). For label free quantification all input files undergo identification based retention time alignment (MapAlignerIdentification), and targeted feature extraction matching ids between runs (FeatureFinderIdentification). In addition, a variant calling file (vcf) can be specified to translate variants into proteins that will be included in the database search and binding predictions on specified alleles (alleles.tsv) using MHCFlurry (Class 1) or MHCNugget (Class 2) can be directly run on the output peptide lists. Moreover, if a vcf file was specified, neoepitopes will automatically be determined and binding predictions can also directly be predicted for them.


nextflow run nf-core/mhcquant --mzmls '*.mzML' --fasta 'SWISSPROT_12_2018.fasta' --alleles 'alleles.tsv' --vcf 'variants.vcf' --include_proteins_from_vcf --predict_class_I --refine_fdr_on_predicted_subset -profile standard,docker


The nf-core/mhcquant pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Running the pipeline
  3. Pipeline HPC Cluster configuration
  4. Output and how to interpret the results
  5. Troubleshooting
  6. Pipeline-specific Troubleshooting


nf-core/mhcquant was originally written by Leon Bichmann,Lukas Heumos,Alexander Peltzer