The output is a single file, qc.html, which summarises the result of the labelcheck run. See an example here
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
- 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.
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.