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.
American Chemical Society
Autores FIOCRUZ - Francisco Gomes Neto e Ana G. C. Neves Ferreira - Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil. AUTHORS - Claudio Iacobuccii#a,#, Christine Piotrowski#a,#, Ruedi Aebersoldb,c, Bruno C. Amarald, Philip Andrewse, Katja Bernfurq, Christoph Borchersf,g,h,i,iD, Nicolas I. Brodief, James E. Brucej,iD, Yong Caoo, Stéphane Chaignepaink, Juan D. Chavezj, Stéphane Claveroll, Jürgen Coxm,iD, Trisha Davisoo, Gianluca Degliespostin, MengQiu Dongo, Nufar Edingerp, Cecilia Emanuelssonq,iD, Marina Gayr, Michael Götzes, Francisco Gomes-Netorr, Fabio C. Gozzod,iD, Craig Gutierrezt, Caroline Hauptu, Albert J. R. Heckv,iD, Franz Herzogw, Lan Huangt,iD, Michael R. Hoopmannx,iD, Nir Kalismanp, Oleg Klykovv,iD, Zdeněk Kukačkay, Fan Liuz, Michael J. MacCossaa, Karl Mechtlerbb,iD, Ravit Mesikap, Robert L. Moritzx,iD, Nagarjuna Nagarajcc, Victor Nesatidd, Ana G. C. Neves-Ferreirarr, Robert Ninnisdd, Petr Nováky,iD, Francis J. O’Reillyee, Matthias Pelzingdd, Evgeniy Petrotchenkof, Lolita Piersimonie, Manolo Plasenciae, Tara Pukalaff,iD, Kasper D. Randgg,iD, Juri Rappsilberee,hh,iD, Dana Reichmannp, Carolin Sailerii, Chris P. Sarnowskib,jj, Richard A. Scheltemav,iD, Carla Schmidtu,iD, David C. Schriemerkk,iD, Yi Shinn, J. Mark Skeheln, Moriya Slavinp, Frank Sobottpp,qq, Victor Solis-Mezarinow, Heike Stephanowitzz, Florian Stengelii, Christian E. Stiegerbb, Esben Trabjerggg, Michael Trnkall, Marta Vilasecar, Rosa Vinermm, Yufei Xiangnn, Sule Yilmazm, Alex Zelteroo,iD, Daniel Ziemianowiczkk, Alexander Leitner*,b,iD, and Andrea Sinz*,a,iD ; AFFILIATIONS:aDepartment 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 bDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland cFaculty of Science, University of Zurich, 8006 Zurich, Switzerland dInstitute of Chemistry, University of Campinas, Campinas São Paulo 13083-970, Brazil eDepartments of Biological Chemistry, Bioinformatics, and Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States fUniversity of Victoria–Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada gDepartment of Biochemistry and Microbiology, University of Victoria, Petch Building, Room 270d, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada hGerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montréal, Quebec H3T 1E2, Canada iProteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montréal, Quebec H3T 1E2, Canada jDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, United States kCBMN, UMR 5248, CNRS, Université de Bordeaux, INP Bordeaux, Pessac 33607, France lCentre de Génomique Fonctionnelle, Plateforme Protéome, Université de Bordeaux, Bordeaux33000, France mComputational Systems Biochemistry Research Group, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany nMRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2,0QH, U.K. oNational Institute of Biological Sciences, Beijing 7 Science Park Road, ZGC Life Science Park, 102206 Beijing, China pDepartment of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel qDepartment of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden rInstitute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain sInstitute for Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle/Saale, Germany tDepartment of Physiology & Biophysics, University of California, Irvine, California 92697, United States uInterdisciplinary 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 vBiomolecular 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 wGene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig Maximilians University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany xInstitute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States yInstitute of Microbiology, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic zLeibniz Institute of Molecular Pharmacology (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany aaDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, United States bbProtein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria ccBiochemistry Core Facility, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany ddAnalytical Biochemistry, CSL Limited, Bio21 Institute, 30 Flemington Road, 3010 Parkville, Melbourne, Australia eeChair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin, 13355 Berlin, Germany ffDiscipline of Chemistry, Faculty of Sciences, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia ggDepartment of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark hhWellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, EH9 3BF Edinburgh, U.K. iiUniversity of Konstanz, Department of Biology, Universitätsstrasse 10, 78457 Konstanz, Germany jjPhD Program in Systems Biology, University of Zurich and ETH Zurich, 8092 Zurich, Switzerland kkDepartment of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, 3330 Hospital Drive North West, Calgary, Alberta T2N 4N1, Canada llUCSF Mass Spectrometry Facility, Genentech Hall, 600 16th Street, San Francisco, California 94158, United States mmThermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States nnDepartment of Cell Biology, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania 15213, United States ooDepartment of Biochemistry,University of Washington, Seattle, Washington 98195, United States ppDepartment of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium qqThe Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, LS2 9JT Leeds, U.K. rrLaboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365 (Moorish Castle), Manguinhos, Rio de Janeiro, Rio de Janeiro 21040-900, Brazil