Crosslinking mass spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats, variable approaches to error control, and insufficient interoperability with global data repositories. Recent advances, especially in false discovery rate models and pipeline benchmarking, show that crosslinking MS data can reach a reliability that matches the demand of integrative structural biology. To drive meaningful progress, however, the community must agree on error estimation, open data formats, and streamlined repository submissions. This perspective highlights these challenges, clarifies remaining barriers, and frames practical next steps. Successful field harmonization will enhance the acceptance of crosslinking MS in the broader biological community and is critical for the dependability of the data, no matter where it is produced.

Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Utrecht Netherlands

Center for Structural Biology Center for Cancer Research National Cancer Institute National Institutes of Health Frederick Maryland USA

Department of Biochemistry and Molecular Biology University of Calgary Alberta Canada

Department of Biochemistry Faculty of Science Charles University Prague Czech Republic; Institute of Microbiology The Czech Academy of Sciences Vestec Czech Republic

Department of Biology University of Konstanz Konstanz Germany; Konstanz Research School Chemical Biology University of Konstanz Konstanz Germany

Department of Chemistry Johns Hopkins University Baltimore Maryland United States; T C Jenkins Department of Biophysics Johns Hopkins University Baltimore Maryland United States

Department of Genome Sciences University of Washington Seattle Washington USA

Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Martin Luther University Halle Wittenberg Halle Germany

Department of Physical and Chemical Sciences University of L'Aquila L'Aquila Italy

Institute of Molecular Systems Biology Department of Biology ETH Zürich Zurich Switzerland

Institute of Structural and Molecular Biology Division of Biosciences University College London London United Kingdom; Institute of Structural and Molecular Biology Birkbeck College University of London London United Kingdom

Research Institute of Molecular Pathology Austrian Academy of Sciences Vienna BioCenter Vienna Austria

Structural Proteomics Human Technopole Milano Italy

Technische Universität Berlin Chair of Bioanalytics Berlin Germany; Wellcome Centre for Cell Biology University of Edinburgh Edinburgh UK; Si M Der Simulierte Mensch a Science Framework of Technische Universität Berlin and Charité Universitätsmedizin Berlin Berlin Germany

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