{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "name": "V. Brennsteiner"
    },
    {
      "name": "L. Diedrich"
    },
    {
      "name": "S. Ben-Moshe"
    },
    {
      "name": "M. Schwoerer"
    },
    {
      "name": "G. Wallmann"
    },
    {
      "name": "W.-F. Zeng"
    },
    {
      "name": "scverse proteomics consortium"
    },
    {
      "name": "F. J. Theis"
    },
    {
      "affs": [
        0
      ],
      "name": "M. Mann"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3mygjjjty7fka.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.11.750886",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750886v1.full",
  "id": "3mygjjjty7fka",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750886v1",
  "language": null,
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1607|Advanced Proteomics Techniques and Applications"
    ]
  ],
  "openalex": "W7212525352",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750886v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-11",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/3mygjjjty7fka.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:56Z",
      "native_id": "10.64898/2026.09.11.750886",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.11.750886v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics",
  "title_text": "AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:56Z",
  "url": "https://research.draconitic.com/paper/3mygjjjty7fka",
  "venue": "bioRxiv",
  "versions": []
}