What happened
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.