Version history

Initial release of nf-core/proteomicslfq, created with the nf-core template.


The initial version of the pipeline features the following steps:

  • (optional) Conversion of spectra data to indexedMzML: Using ThermoRawFileParser if Thermo Raw or using OpenMS’ FileConverter if just an index is missing
  • (optional) Decoy database generation for the provided DB (fasta) with OpenMS
  • Database search with either MSGF+ and/or Comet through OpenMS adapters
  • Re-mapping potentially identified peptides to the input database for consistency and error-checking (using OpenMS’ PeptideIndexer)
  • PSM rescoring using PSMFeatureExtractor and Percolator or a PeptideProphet-like distribution fitting approach in OpenMS
  • If multiple search engines were chosen, the results are combined with OpenMS’ ConsensusID
  • If multiple search engines were chosen, a combined FDR is calculated
  • Single run PSM/Peptide-level FDR filtering
  • If localization of modifications was requested, Luciphor2 is applied via the OpenMS adapter
  • Protein inference and labelfree quantification based on spectral counting or MS1 feature detection, alignment and integration with OpenMS’ ProteomicsLFQ. Performs an additional experiment-wide FDR filter on protein level (and if requested peptide/PSM level).

Known issues

If you experience nextflow running forever after a failed step, try settings errorStrategy = terminate. See the corresponding nextflow issue.