A Python package for proteomics quality control (QC) of mass spectrometry data. It provides fast data parsing, protein/peptide-level QC metrics, run-level flagging, and HTML/JSON/text report generation for FragPipe, Spectronaut, and generic proteomics matrices.
- 🔬 Proteomics matrix parsing — FragPipe, Spectronaut, or generic wide abundance tables
- 📊 Run-level QC metrics — identified proteins, missingness, PCA, and sample correlations
⚠️ Flagging of problematic runs — low IDs, high missingness, and abundance outliers- 🎯 FragPipe advanced QC — PSM, peptide, and contamination metrics for DDA searches
- 🧾 Multi-format reports — JSON, plain text, and HTML dashboards
- 🖥️ CLI interface — simple sample-qc command-line workflow
�ash pip install -e .
�ash sample-qc run data/mock_fragpipe.tsv --format all sample-qc run data/mock_spectronaut.tsv --format html sample-qc run data/FragPipe_result1 --format json sample-qc version
Supported input types:
- FragPipe combined_protein.tsv file or project directory
- Spectronaut exported report file (wide or long format)
- Generic proteomics matrix with protein/peptide identifier as the first column
Example files are available under data/.
- json — raw QC metrics for downstream processing
- html — interactive dashboard report
- ext — compact console-friendly summary
sample_QC/ ├── sample_qc/ # Core Python package │ ├── __init__.py │ ├── cli.py # Click CLI │ ├── metrics.py # Proteomics QC metric computations │ ├── parser.py # Proteomics input parsers │ └── report.py # Report generation ├── tests/ # Unit tests ├── data/ # Proteomics example data ├── pyproject.toml # Package metadata └── README.md
�ash pip install -e . pytest tests/ -v
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