{
  "abstract": "In a community effort, we audited error control in twelve crosslinking mass spectrometry pipelines using two ground-truth designs that expose a lower bound on false identifications. Some pipelines passed, whereas for others these verifiably false identifications alone exceeded the requested false discovery rate up to 29-fold at the protein–protein interaction level. The audit also tracked improvement between software versions, supporting its use for regression testing.",
  "abstract_shown": true,
  "affiliations": [
    "Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany.",
    "Si-M/“Der Simulierte Mensch”, a Science Framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany.",
    "Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.",
    "Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, Hagenberg, 4232, Austria.",
    "University of Washington, Seattle, WA, USA.",
    "Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil",
    "Department of Pharmaceutical Chemistry, University of California, San Francisco, USA.",
    "Department of Chemistry, Unicamp, São Paulo, Brazil",
    "Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, and Netherlands Proteomics Center, Utrecht, the Netherlands.",
    "Institute for Systems Biology, Seattle, WA, USA.",
    "Department of Physical and Chemical Sciences, University of L’Aquila, L’Aquila, Italy.",
    "Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP) 12489 Berlin, Germany.",
    "Research Institute of Molecular Pathology (IMP), The Vienna Biocenter, Dr. Bohrgasse 7, Vienna, A-1030, Austria.",
    "Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.",
    "Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.",
    "current affiliation: Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Potsdam-Golm, Germany",
    "Arafel Consulting LLC, Seattle, Washington. USA.",
    "Thermo Fisher Scientific, San Jose, CA, USA."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 26,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Lutz Fischer",
      "orcid": "0000-0003-4978-0864"
    },
    {
      "affs": [
        2
      ],
      "name": "Bruno C. Amaral"
    },
    {
      "affs": [
        3
      ],
      "name": "Micha Johannes Birklbauer",
      "orcid": "0009-0005-1051-179X"
    },
    {
      "affs": [
        4
      ],
      "name": "James E. Bruce",
      "orcid": "0000-0001-6441-6089"
    },
    {
      "affs": [
        5
      ],
      "name": "Paulo C Carvalho",
      "orcid": "0000-0001-6530-3350"
    },
    {
      "affs": [
        6
      ],
      "name": "Robert J. Chalkley",
      "orcid": "0000-0002-9757-7302"
    },
    {
      "affs": [
        5
      ],
      "name": "Milan A Clasen",
      "orcid": "0000-0002-9118-7581"
    },
    {
      "affs": [
        3
      ],
      "name": "Viktoria Dorfer",
      "orcid": "0000-0002-5332-5701"
    },
    {
      "affs": [
        7
      ],
      "name": "Fabio C Gozzo",
      "orcid": "0000-0002-5270-4427"
    },
    {
      "affs": [
        8
      ],
      "name": "A.J.R Heck"
    },
    {
      "affs": [
        9
      ],
      "name": "Michael R. Hoopmann",
      "orcid": "0000-0001-7029-7792"
    },
    {
      "affs": [
        10
      ],
      "name": "Claudio Iacobucci"
    },
    {
      "affs": [
        4
      ],
      "name": "Andrew Keller",
      "orcid": "0000-0003-3939-3692"
    },
    {
      "affs": [
        0
      ],
      "name": "Lars Kolbowski",
      "orcid": "0000-0001-6819-6570"
    },
    {
      "affs": [
        0
      ],
      "name": "Swantje Lenz",
      "orcid": "0000-0002-8839-5371"
    },
    {
      "affs": [
        5
      ],
      "name": "Diogo Borges Lima",
      "orcid": "0000-0001-6056-0825"
    },
    {
      "affs": [
        11
      ],
      "name": "Fan Liu"
    },
    {
      "affs": [
        12,
        13,
        14
      ],
      "name": "Karl Mechtler"
    },
    {
      "affs": [
        9
      ],
      "name": "Robert L. Moritz",
      "orcid": "0000-0002-3216-9447"
    },
    {
      "affs": [
        12,
        15
      ],
      "name": "Fränze Müller",
      "orcid": "0000-0003-3764-3547"
    },
    {
      "affs": [
        11
      ],
      "name": "Julia Ruta",
      "orcid": "0009-0007-0524-6885"
    },
    {
      "affs": [
        2
      ],
      "name": "David C. Schriemer"
    },
    {
      "affs": [
        16
      ],
      "name": "David D. Shteynberg",
      "orcid": "0000-0001-7982-0498"
    },
    {
      "affs": [
        6
      ],
      "name": "Michael J. Trnka",
      "orcid": "0000-0002-8808-5146"
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    {
      "affs": [
        17
      ],
      "name": "Rosa Viner",
      "orcid": "0000-0003-0550-5545"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Juri Rappsilber",
      "orcid": "0000-0001-5999-1310"
    }
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  "bibtex": "https://research.draconitic.com/paper/a19mcma3stqey.bib",
  "cited_by": 1,
  "doi": "10.1101/2025.04.27.649519",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13733680/",
  "id": "a19mcma3stqey",
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  "language": "en",
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  "pdf_url": "https://www.biorxiv.org/content/biorxiv/early/2025/04/28/2025.04.27.649519.full.pdf",
  "pmcid": "PMC13733680",
  "pmid": "42990131",
  "published": "2026-10-28",
  "publisher": "Cold Spring Harbor Laboratory Preprints",
  "ris": "https://research.draconitic.com/paper/a19mcma3stqey.ris",
  "sources": [
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      "url": "https://doi.org/10.1101/2025.04.27.649519"
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  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:1607|Advanced Proteomics Techniques and Applications",
      "subfield": "physical"
    }
  ],
  "title": "A community audit of error control in crosslinking mass spectrometry",
  "title_text": "A community audit of error control in crosslinking mass spectrometry",
  "type": "preprint",
  "updated_at": "2026-11-08T12:23:24Z",
  "url": "https://research.draconitic.com/paper/a19mcma3stqey",
  "venue": "bioRxiv",
  "versions": []
}