Cross-linking mass spectrometry (MS) has substantially matured as a method over the past 2 decades through parallel development in multiple labs, demonstrating its applicability to protein structure determination, conformation analysis, and mapping protein interactions in complex mixtures. Cross-linking MS has become a much-appreciated and routinely applied tool, especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Cross-linking MS for which guidelines should be developed as part of a Cross-linking MS standards initiative.

Bijvoet Centre for Biomolecular Research Faculty of Science Chemistry Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands

Bioanalytical Mass Spectrometry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

Bioanalytics Institute of Biotechnology Technische Universität Berlin 13355 Berlin Germany

Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University 3584 CH Utrecht The Netherlands; Netherlands Proteomics Centre Utrecht University 3584 CH Utrecht The Netherlands

Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University Institute of Microbiology The Czech Academy of Sciences 252 50 Vestec Czech Republic

Computational Systems Biochemistry Research Group Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany

Department of Biochemistry and Molecular Biology University of Calgary Calgary AB T2N 4N1 Canada; Robson DNA Science Centre Arnie Charbonneau Cancer Institute University of Calgary Calgary AB T2N 4N1 Canada; Department of Chemistry University of Calgary Calgary AB T2N 4N1 Canada

Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California San Francisco 1700 4th Street San Francisco CA 94143 USA

Department of Biological Chemistry Institute of Life Sciences Hebrew University of Jerusalem Jerusalem 91904 Israel

Department of Biology Institute of Molecular Systems Biology ETH Zurich 8093 Zurich Switzerland

Department of Computer Science University of Tübingen Sand 14 72076 Tübingen Germany; Biomolecular Interactions Max Planck Institute for Developmental Biology Max Planck Ring 5 72076 Tübingen Germany

Department of Computer Science University of Tübingen Sand 14 72076 Tübingen Germany; Institute for Bioinformatics and Medical Informatics University of Tübingen Sand 14 72076 Tübingen Germany; Institute for Translational Bioinformatics University Hospital Tübingen Hoppe Seyler Strasse 9 72076 Tübingen Germany; Biomolecular Interactions Max Planck Institute for Developmental Biology Max Planck Ring 5 72076 Tübingen Germany

Department of Pharmaceutical Chemistry and Bioanalytics Charles Tanford Protein Center Martin Luther University Halle Wittenberg Kurt Mothes Strasse 3a 06120 Halle Saale Germany

Department of Pharmaceutical Chemistry University of California San Francisco 600 16th Street Genentech Hall Suite N472A San Francisco CA 94143 2240 USA

Department of Physiology and Biophysics University of California Irvine Irvine CA 92697 USA

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK

Graduate School of Pharmaceutical Sciences Kyoto University Kyoto 606 8501 Japan

Institut Pasteur CNRS USR 2000 Mass Spectrometry for Biology Unit 28 Rue du Dr Roux 75 015 Paris France

Institute for Systems Biology 401 Terry Avenue North Seattle WA 98109 USA

Institute of Chemistry University of Campinas Campinas SP 13083 970 Brazil

Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street Liverpool L69 7ZB UK

Institute of Structural and Molecular Biology Birkbeck College University of London Malet Street London WC1E 7HX UK; Institute of Structural and Molecular Biology Division of Biosciences University College London Gower Street London WC1E 6BT UK

Interdisciplinary Research Center HALOmem Institute for Biochemistry and Biotechnology Martin Luther University Halle Wittenberg Kurt Mothes Strasse 3a 06120 Halle Saale Germany

National Institute of Biological Sciences Beijing Beijing 102206 China

Research Institute of Molecular Pathology Campus Vienna Biocenter 1 1030 Vienna Austria

School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney 2052 Australia

School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology University of Leeds Leeds LS2 9JT UK; Department of Chemistry Biomolecular and Analytical Mass Spectrometry Group University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium

Segal Cancer Proteomics Centre Lady Davis Institute Jewish General Hospital McGill University Montreal QC H3T 1E2 Canada; Center for Computational and Data Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow 121205 Russia

Thermo Fisher Scientific 355 River Oaks Parkway San Jose CA 95134 USA

University of Konstanz Department of Biology Universitätsstrasse 10 78457 Konstanz Germany; Konstanz Research School Chemical Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany

University of Victoria Genome British Columbia Proteomics Centre University of Victoria Victoria BC V8Z 7X8 Canada; Department of Biochemistry and Microbiology University of Victoria Victoria BC V8P 5C2 Canada; Segal Cancer Proteomics Centre Lady Davis Institute Jewish General Hospital McGill University Montreal QC H3T 1E2 Canada; Gerald Bronfman Department of Oncology Jewish General Hospital McGill University Montreal QC H3T 1E2 Canada; Center for Computational and Data Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow 121205 Russia

Wellcome Centre for Cell Biology School of Biological Sciences University of Edinburgh Edinburgh EH9 3BF Scotland UK

Wellcome Centre for Cell Biology School of Biological Sciences University of Edinburgh Edinburgh EH9 3BF Scotland UK; Bioanalytics Institute of Biotechnology Technische Universität Berlin 13355 Berlin Germany

References provided by Crossref.org

A Roadmap for Improving Reliability and Data Sharing in Crosslinking Mass Spectrometry