quantms-rescoring: Python scripts and helpers for the quantMS workflow
Project description
quantms-rescoring
quantms-rescoring is a Python tool for rescoring peptide-spectrum matches (PSMs) in idXML files. It is part of the quantms ecosystem package and leverages the MS²Rescore framework to improve identification confidence in proteomics data analysis.
Features
- Enhanced Rescoring: Utilizes advanced rescoring engines like Percolator to refine PSM scores.
- Flexible Feature Generators: Supports feature extraction using tools like MS²PIP, DeepLC, and custom generators.
- Metadata Retention: Preserves essential metadata from the input idXML files.
- Error Handling: Skips invalid PSMs and logs issues for transparent processing.
- Seamless Integration: Built to integrate into proteomics workflows.
Installation
To use quantms-rescoring, ensure the following dependencies are installed:
- Python 3.8+
- click
- pyopenms
- ms2rescore
- psm_utils
Issues and Contributions
For any issues or contributions, please open an issue in the GitHub repository - we use the quantms repo to control all issues—or PR in the GitHub repository.
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