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bioRxiv · 10.64898/2026.03.31.715273

ProteoPy: an AnnData-based framework for integrated proteomics analysis

Fichtner, I. D.·Temesvari-Nagy, L.·Sahm, F.·Gerstung, M.·Bludau, I.
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Abstract

SummaryProteoPy 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 implementationProteoPy is implemented in Python 3 and publicly available on GitHub: https://github.com/UKHD-NP/proteopy under the Apache 2.0 license. Contactisabell.bludau@med.uni-heidelberg.de Supplementary informationTutorial notebooks for ProteoPy are included as supplementary data and are also available on GitHub: https://github.com/UKHD-NP/proteopy/tree/main/docs/tutorials.

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Fichtner, I. D., Temesvari-Nagy, L., Sahm, F., Gerstung, M., Bludau, I.. 2026-04-01. ProteoPy: an AnnData-based framework for integrated proteomics analysis. https://doi.org/10.64898/2026.03.31.715273

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