The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

Analytical Biochemistry CSL Limited Bio21 Institute 30 Flemington Road 3010 Parkville Melbourne Australia

Biochemistry Core Facility Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany

Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences University of Utrecht and Netherlands Proteomics Centre Padualaan 8 3584 CH Utrecht The Netherlands

CBMN UMR 5248 CNRS Université de Bordeaux INP Bordeaux Pessac 33607 France

Centre de Génomique Fonctionnelle Plateforme Protéome Université de Bordeaux Bordeaux 33000 France

Chair of Bioanalytics Institute of Biotechnology Technische Universität Berlin 13355 Berlin Germany

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

Department of Biochemistry and Microbiology University of Victoria Petch Building Room 270d 3800 Finnerty Road Victoria British Columbia V8P 5C2 Canada

Department of Biochemistry and Molecular Biology Robson DNA Science Centre University of Calgary 3330 Hospital Drive North West Calgary Alberta T2N 4N1 Canada

Department of Biochemistry and Structural Biology Center for Molecular Protein Science Lund University 221 00 Lund Sweden

Department of Biochemistry University of Washington Seattle Washington 98195 United States

Department of Biological Chemistry The Alexander Silberman Institute of Life Sciences Safra Campus Givat Ram The Hebrew University of Jerusalem Jerusalem 91904 Israel

Department of Biology Institute of Molecular Systems Biology ETH Zurich Otto Stern Weg 3 8093 Zurich Switzerland

Department of Cell Biology University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15213 United States

Department of Chemistry University of Antwerp Groenenborgerlaan 171 2020 Antwerp Belgium

Department of Genome Sciences University of Washington Seattle Washington 98195 United States

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

Department of Pharmacy University of Copenhagen 2100 Copenhagen Denmark

Department of Physiology and Biophysics University of California Irvine California 92697 United States

Departments of Biological Chemistry Bioinformatics and Chemistry University of Michigan Ann Arbor Michigan 48109 United States

Discipline of Chemistry Faculty of Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia

Faculty of Science University of Zurich 8006 Zurich Switzerland

Gene Center Munich Department of Biochemistry Faculty of Chemistry and Pharmacy Ludwig Maximilians University of Munich Feodor Lynen Strasse 25 81377 Munich Germany

Gerald Bronfman Department of Oncology Jewish General Hospital McGill University 3755 Côte Ste Catherine Road Montréal Quebec H3T 1E2 Canada

Institute for Biochemistry and Biotechnology Charles Tanford Protein Center Martin Luther University Halle Wittenberg Kurt Mothes Strasse 3a 06120 Halle Saale Germany

Institute for Research in Biomedicine Baldiri Reixac 10 08028 Barcelona Spain

Institute for Systems Biology 401 Terry Avenue North Seattle Washington 98109 United States

Institute of Chemistry University of Campinas Campinas São Paulo 13083 970 Brazil

Institute of Microbiology BIOCEV Prumyslova 595 252 50 Vestec Czech Republic

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

Laboratory of Toxinology Oswaldo Cruz Institute Fiocruz Avenida Brasil 4365 Manguinhos Rio de Janeiro Rio de Janeiro 21040 900 Brazil

Leibniz Institute of Molecular Pharmacology Robert Rössle Strasse 10 13125 Berlin Germany

MRC Laboratory of Molecular Biology Cambridge Biomedical Campus Francis Crick Avenue Cambridge CB2 0QH U K

National Institute of Biological Sciences Beijing 7 Science Park Road ZGC Life Science Park 102206 Beijing China

PhD Program in Systems Biology University of Zurich and ETH Zurich 8092 Zurich Switzerland

Protein Chemistry Facility Research Institute of Molecular Pathology Dr Bohr Gasse 3 1030 Vienna Austria

Proteomics Centre Segal Cancer Centre Lady Davis Institute Jewish General Hospital McGill University 3755 Côte Ste Catherine Road Montréal Quebec H3T 1E2 Canada

The Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology University of Leeds LS2 9JT Leeds U K

Thermo Fisher Scientific 355 River Oaks Parkway San Jose California 95134 United States

UCSF Mass Spectrometry Facility Genentech Hall 600 16th Street San Francisco California 94158 United States

University of Konstanz Department of Biology Universitätsstrasse 10 78457 Konstanz Germany

University of Victoria Genome British Columbia Proteomics Centre Vancouver Island Technology Park Victoria British Columbia V8Z 7X8 Canada

Wellcome Trust Centre for Cell Biology School of Biological Sciences University of Edinburgh EH9 3BF Edinburgh U K

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