ProteoPy: an AnnData-based framework for integrated proteomics analysis

Abstract Summary ProteoPy is a lightweight Python library for protein- and peptide-level quantitative proteomics analysis, built around the AnnData class as its core data structure. It streamlines data import, preprocessing, and differential analysis while preserving all metadata within a single object. A reimplementation of our previously published COPF algorithm enables proteoform group inference directly from peptide-level data, facilitating the identification of proteoform-specific regulation and isoform usage. Designed for accessibility and flexibility, ProteoPy simplifies analysis for non-specialists and provides an extensible foundation for advanced proteomics workflows, seamlessly integrating with the scanpy and muon ecosystems for reproducible and scalable multi-omics analysis. Availability and implementation ProteoPy is implemented in Python 3 and publicly available on GitHub: https://github.com/UKHD-NP/proteopy under the Apache 2.0 license. Contact isabell.bludau@med.uni-heidelberg.de Supplementary information Tutorial notebooks for ProteoPy are included as supplementary data and are also available on GitHub: https://github.com/UKHD-NP/proteopy/tree/main/docs/tutorials .