Open access
AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics
Vincenth Brennsteiner
L. Diedrich
S. Ben-Moshe
Magnus Schwörer
G. Wallmann
Wen-Feng Zeng
Fabian J. Theis
Matthias Mann
Biology
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. Code Availability: https://github.com/MannLabs/AlphaPeptTools.git