We here present a drastically improved version of the MS 2 Rescore framework for datadriven peptide identification rescoring. Its highly modular code base and new features ensure a user-friendly experience, facilitate rescoring quality control (QC), and guarantee more reproducible results. Moreover, this new version of MS 2 Rescore is highly flexible, can be smoothly implemented into existing workflows, and can be easily extended to support new feature generators or rescoring tools. Additionally, we show how recent improvements in the MS Amanda search engine streamline its integration with identification post-processing tools, such as MS 2 Rescore. Finally, we demonstrate the capabilities of MS Amanda and MS 2 Rescore on a recent single-cell proteomics data set.