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bioRxiv · 10.64898/2026.09.11.750886

AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics

Brennsteiner, V.·Diedrich, L.·Ben-Moshe, S.·Schwoerer, M.·Wallmann, G.·Zeng, W.-F.·scverse proteomics consortium,·Theis, F. J.·Mann, M.
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Abstract

Mass spectrometry (MS)-based proteomics now routinely profiles proteomes at scale, but extracting biological insight and integrating complementary modalities remains challenging. Here, we present AlphaPeptTools, a Python package for the analysis of MS-proteomics data built on the AnnData data structure of the scverse. AlphaPeptTools implements scalable and modular strategies for MS-data ingestion, quality control, preprocessing, and statistical analysis while seamlessly integrating with the scverse ecosystem, unlocking multi-level, spatial, and multimodal analyses.

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Brennsteiner, V., Diedrich, L., Ben-Moshe, S., Schwoerer, M., Wallmann, G., Zeng, W.-F., scverse proteomics consortium,, Theis, F. J., Mann, M.. 2026-09-13. AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics. https://doi.org/10.64898/2026.09.11.750886

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