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Anal Chem. 2019 Jun 4;91(11):6953-6961. doi: 10.1021/acs.analchem.9b00658. Epub 2019 May 22.

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.

Author information

1
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.
2
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.
3
Faculty of Science , University of Zurich , 8006 Zurich , Switzerland.
4
Institute of Chemistry , University of Campinas , Campinas São Paulo 13083-970 , Brazil.
5
Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.
6
Department of Biochemistry and Structural Biology, Center for Molecular Protein Science , Lund University , 221 00 Lund , Sweden.
7
University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada.
8
Department of Biochemistry and Microbiology , University of Victoria , Petch Building, Room 270d, 3800 Finnerty Road , Victoria , British Columbia V8P 5C2 , Canada.
9
Gerald Bronfman Department of Oncology, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada.
10
Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada.
11
Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.
12
National Institute of Biological Sciences , Beijing 7 Science Park Road, ZGC Life Science Park , 102206 Beijing , China.
13
CBMN, UMR 5248, CNRS , Université de Bordeaux, INP Bordeaux , Pessac 33607 , France.
14
Centre de Génomique Fonctionnelle, Plateforme Protéome , Université de Bordeaux , Bordeaux 33000 , France.
15
Computational Systems Biochemistry Research Group , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany.
16
Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States.
17
MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K.
18
Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel.
19
Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10 , 08028 Barcelona , Spain.
20
Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany.
21
Laboratory of Toxinology , Oswaldo Cruz Institute , Fiocruz, Avenida Brasil 4365 (Moorish Castle) , Manguinhos, Rio de Janeiro , Rio de Janeiro 21040-900 , Brazil.
22
Department of Physiology & Biophysics , University of California , Irvine , California 92697 , United States.
23
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.
24
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.
25
Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy , Ludwig Maximilians University of Munich , Feodor-Lynen-Strasse 25 , 81377 Munich , Germany.
26
Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States.
27
Institute of Microbiology , BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic.
28
Leibniz Institute of Molecular Pharmacology (FMP) , Robert-Rössle-Strasse 10 , 13125 Berlin , Germany.
29
Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria.
30
Biochemistry Core Facility , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany.
31
Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia.
32
Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin , 13355 Berlin , Germany.
33
Discipline of Chemistry, Faculty of Sciences , University of Adelaide , North Terrace, Adelaide , South Australia 5005 , Australia.
34
Department of Pharmacy , University of Copenhagen , 2100 Copenhagen , Denmark.
35
Wellcome Trust Centre for Cell Biology, School of Biological Sciences , University of Edinburgh , EH9 3BF Edinburgh , U.K.
36
University of Konstanz , Department of Biology , Universitätsstrasse 10 , 78457 Konstanz , Germany.
37
PhD Program in Systems Biology , University of Zurich and ETH Zurich , 8092 Zurich , Switzerland.
38
Department of Biochemistry & Molecular Biology, Robson DNA Science Centre , University of Calgary , 3330 Hospital Drive North West , Calgary , Alberta T2N 4N1 , Canada.
39
Department of Cell Biology , University of Pittsburgh, School of Medicine , Pittsburgh , Pennsylvania 15213 , United States.
40
Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , 2020 Antwerp , Belgium.
41
The Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology , University of Leeds , LS2 9JT Leeds , U.K.
42
UCSF Mass Spectrometry Facility , Genentech Hall, 600 16th Street , San Francisco , California 94158 , United States.
43
Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States.

Abstract

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.

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