Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
⚠️ Note: This is the documentation for the fully redeveloped version 3.0 of MS²Rescore, which is now in the beta stage. While MS²Rescore 3.0 has been drastically improved over the previous version, you might run into some unforeseen issues. Please report any issues you encounter on the issue tracker or post your questions on the GitHub Discussions forum.
MS²Rescore performs ultra-sensitive peptide identification rescoring with LC-MS predictors such as MS²PIP and DeepLC, and with ML-driven rescoring engines Percolator or Mokapot. This results in more confident peptide identifications, which allows you to get more peptide IDs at the same false discovery rate (FDR) threshold, or to set a more stringent FDR threshold while still retaining a similar number of peptide IDs. MS²Rescore is ideal for challenging proteomics identification workflows, such as proteogenomics, metaproteomics, or immunopeptidomics.
Latest MS²Rescore publication:
MS2Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates. Arthur Declercq, Robbin Bouwmeester, Aurélie Hirschler, Christine Carapito, Sven Degroeve, Lennart Martens, and Ralf Gabriels. Molecular & Cellular Proteomics (2021) doi:10.1016/j.mcpro.2022.100266 >
Original publication describing the concept of rescoring with predicted spectra:
Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions. Ana S C Silva, Robbin Bouwmeester, Lennart Martens, and Sven Degroeve. Bioinformatics (2019) doi:10.1093/bioinformatics/btz383 >
To replicate the experiments described in this article, check out the publication branch of the repository.
The desktop application can be installed on Windows with a one-click installer.
The Python package and command line interface can be installed with
Check out the full documentation to get started.
Questions or issues?
Have questions on how to apply MS²Rescore on your data? Or ran into issues while using MS²Rescore? Post your questions on the GitHub Discussions forum and we are happy to help!