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quantms-rescoring

Python package codecov PyPI version License

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.