Skip to content

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 - MS2 spectra are searched against a user-supplied FASTA database, without and if necessary with (static) 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.