Output

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+

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

Percolator

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

OpenMS

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/Kronik

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

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.