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.
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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