This document describes the output produced by the pipeline.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

  • MSGF+ - Peptide identification search engine
  • Percolator - Target-decoy scoring
  • OpenMS - Quantification of isobaric tags
  • Hardklor/Kronik - Quantification of precursor peptides
  • Msstitch - Post processing, protein inference


MSGF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.


Percolator is a semi-supervised machine learning program to better separate target vs decoy peptide scoring.


OpenMS is a library that contains a large amount of tools for MS data analysis. This workflow uses its isobaric quantification program to extract peak intenstities for isobaric multiplex samples.


Hardklor identifies peptide features in MS1 data by reducing isotope distributions to a single monoisotopic mass. It in tandem with its Kronik utility (which summarizes the Hardklor results from LC/MS data) can be used to quantify MS1 peptide features.


Msstitch is a package to merge identification and quantification PSM data, reporting PSM, peptide, protein and gene tables, adding q-values, quantitfications, protein groups, etc.