QPX¶
A standardized format and toolkit for mass spectrometry proteomics data
What is QPX?¶
QPX is a comprehensive ecosystem for proteomics data that provides:
- Standardized Data Format: Parquet-based format for efficient storage and processing of proteomics data
- Universal Converter: Convert data from MaxQuant, DIA-NN, FragPipe, OpenMS, and more
- Complete Toolkit: Process, analyze, visualize, and share your proteomics results
- Python API & CLI: Flexible tools for both programmatic and command-line usage
Architecture Overview¶
qpx provides a comprehensive proteomics data processing architecture with core modules for data conversion, transformation, visualization, statistical analysis, and project management.
Supported Input Formats¶
| Software | PSM | Feature | Protein Group |
|---|---|---|---|
| MaxQuant | msms.txt | evidence.txt | proteinGroups.txt |
| DIA-NN | report.tsv | report.tsv | pg_matrix.tsv |
| FragPipe | psm.tsv | - | - |
| OpenMS | idXML | - | - |
| mzTab | PSM section | PEP section | PRT section |
All conversions produce standardized Parquet and AnnData files following the QPX specification.
Documentation¶
| Section | Description |
|---|---|
| Quick Start | Installation and basic usage |
| Format Specification | Data format schemas and specifications |
| User Guide | CLI reference and command documentation |
| Examples & Tutorials | Usage examples and integrations |
| Troubleshooting | Common issues and solutions |
| Community & Support | Get help, contribute, license & acknowledgments |
Ready to get started? Install qpx and check out the examples!