# quantms-rescoring
[](https://github.com/bigbio/quantms-rescoring/actions/workflows/python-package.yml)
[](https://codecov.io/gh/bigbio/quantms-rescoring)
[](https://badge.fury.io/py/quantms-rescoring)
[](https://opensource.org/licenses/Apache-2.0)
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](https://github.com/bigbio/quantms/issues) - we use the quantms repo to control all issues—or PR in the [GitHub repository](https://github.com/bigbio/quantms-rescoring/pulls).
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