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PreprintCC BY-NCbioRxiv

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

  • V. Brennsteiner
  • L. Diedrich
  • S. Ben-Moshe
  • M. Schwoerer
  • G. Wallmann
  • W.-F. Zeng
  • scverse proteomics consortium
  • F. J. Theis
  • M. Mann1
  1. 1Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry
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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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Cite

BibTeXRIS
BibTeX
@misc{brennsteiner2026alphapepttools,
  title = {{AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics}},
  author = {V. Brennsteiner and L. Diedrich and S. Ben-Moshe and M. Schwoerer and G. Wallmann and W.-F. Zeng and scverse proteomics consortium and F. J. Theis and M. Mann},
  howpublished = {bioRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.11.750886},
  url = {https://www.biorxiv.org/content/10.64898/2026.09.11.750886v1},
  note = {CC BY-NC},
}
RIS
TY  - UNPB
TI  - AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics
AU  - V. Brennsteiner
AU  - L. Diedrich
AU  - S. Ben-Moshe
AU  - M. Schwoerer
AU  - G. Wallmann
AU  - W.-F. Zeng
AU  - scverse proteomics consortium
AU  - F. J. Theis
AU  - M. Mann
PY  - 2026
DA  - 2026/09/11
PB  - bioRxiv
DO  - 10.64898/2026.09.11.750886
UR  - https://www.biorxiv.org/content/10.64898/2026.09.11.750886v1
AB  - 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.
ER  -