Plate IV.9 · Publications
AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics
Preprint in bioRxiv, 13 September 2026.
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
Cite
@misc{brennsteiner2026alphapepttools,
title = {{AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics}},
author = {Brennsteiner, Vincenth and Diedrich, Lucas and Ben-Moshe, Shani and Schwörer, Magnus and Wallmann, Georg and Zeng, Wen-Feng and scverse proteomics consortium and Theis, Fabian J and Mann, Matthias},
howpublished = {bioRxiv},
publisher = {openRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.11.750886},
url = {https://doi.org/10.64898/2026.09.11.750886},
note = {Preprint}
}