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nf-core/macproqc

nf-core/macproqc (Mass Centric Proteomics Quality Control) is a bioinformatics pipeline for comprehensive quality control of mass spectrometry-based proteomics experiments. It accepts raw instrument files from Thermo Fisher (.raw) and Bruker (.d) instruments as well as pre-converted mzML files and produces a rich set of QC metrics, interactive visualisations, and standardised mzQC output.

The pipeline performs the following main steps:

  • Spectra preparation — raw vendor files are decompressed and converted to the open mzML format using ThermoRawFileParser (Thermo) or tdf2mzml (Bruker).
  • Raw-data QC metrics extraction (migrating) — MS1/MS2 spectrum counts, TIC quartiles, precursor charge distributions, retention-time coverage and more are extracted from the mzML files using pyOpenMS.
  • Peptide identification (migrating) — MS2 spectra are searched against a user-supplied FASTA database, without and if necessary with label information.
  • FDR filtering and protein inference (migrating) — PSM-level results are filtered at 1 % FDR and protein groups are inferred with PIA — Protein Inference Algorithms.
  • QC metrics for peptide features (migrating) — OpenMS identifies isotope features; found features are mapped to identifications to yield identification rates and QC metrics are extracted.
  • mzQC output (migrating) — all QC metrics are exported in the standardised mzQC format for interoperability.
  • Visualisation (migrating) — an interactive report with barplots, TIC overlays, ion maps and PCA plots is generated using Plotly.

Documentation

  • Usage — how to run the pipeline, samplesheet format, and all parameters.
  • Parameters — full parameter reference generated from the pipeline schema.
  • Output — description of all output files and directories.
  • Contributing — how to contribute to the pipeline.