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Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

View ORCID ProfileClaudio Iacobucci, Christine Piotrowski, Ruedi Aebersold, Bruno C. Amaral, Philip Andrews, Christoph Borchers, Nicolas I. Brodie, James E. Bruce, Stephane Chaignepain, Juan D. Chavez, Stephane Claverol, Juergen Cox, Gianluca Degliesposti, Meng Q. Dong, Nufar Edinger, Cecilia Emanuelsson, Marina Gay, Michael Goetze, Fabio C. Gozzo, Craig Gutierrez, Caroline Haupt, Albert J. R. Heck, Franz Herzog, Lan Huang, Michael R. Hoopmann, Nir Kalisman, Oleg Klykov, Zdenek Kukacka, Fan Liu, Michael J. MacCoss, Karl Mechtler, Ravit Mesika, Robert L. Moritz, Nagarjuna Nagaraj, Victor Nesati, Robert Ninnis, Petr Novak, Francis J. O'Reilly, Matthias Pelzing, Evgeniy Petrotchenko, Lolita Piersimoni, Manolo Plasencia, Tara Pukala, Kasper D. Rand, Juri Rappsilber, Dana Reichmann, Caroline Sailer, Chris P. Sarnowski, Richard A. Scheltema, Carla Schmidt, David C. Schriemer, Yi Shi, Mark J. Skehel, Moriya Slavin, Frank Sobott, Victor Solis-Mezarino, Heike Stephanowitz, Florian Stengel, Christian E. Stieger, Michael Trnka, Marta Vilaseca, Rosa Viner, Yufei Xiang, Sule Yilmaz, Alex Zelter, Daniel Ziemianowicz, View ORCID ProfileAlexander Leitner, View ORCID ProfileAndrea Sinz
doi: https://doi.org/10.1101/424697
Claudio Iacobucci
Dept. Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Prot;
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Christine Piotrowski
Dept. Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Prot;
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Ruedi Aebersold
Dept. Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 80;
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Bruno C. Amaral
Institute of Chemistry, University of Campinas, Campinas SP, 13083-970, Brazil;
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Philip Andrews
Depts. Biological Chemistry, Bioinformatics, and Chemistry, University of Michigan, Ann Arbor;
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Christoph Borchers
University of Victoria -Genome British Columbia Proteomics Centre, Vancouver Island Technology Park;
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Nicolas I. Brodie
University of Victoria -Genome British Columbia Proteomics Centre, Vancouver Island Technology Park;
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James E. Bruce
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA;
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Stephane Chaignepain
CBMN , UMR 5248, CNRS, Universite de Bordeaux, INP Bordeaux, Pessac, France;
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Juan D. Chavez
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA;
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Stephane Claverol
Centre de Genomique Fonctionnelle, Plateforme Proteome, Universite de Bordeaux, Bordeaux, France;
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Juergen Cox
Computational Systems Biochemistry Res. Group, Max-Planck-Institute of Biochemistry, Am Klopfers;
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Gianluca Degliesposti
MRC Laboratory Molecular Biology, Cambridge Biomedical Campus, Cambridge;
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Meng Q. Dong
National Institute of Biological Sciences, Beijing, 7 Science Park Road, ZGC Life Science Park, 1022;
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Nufar Edinger
Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus;
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Cecilia Emanuelsson
Dept. Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University;
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Marina Gay
Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology;
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Michael Goetze
Institute Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University;
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Fabio C. Gozzo
Institute of Chemistry, University of Campinas, Campinas SP, 13083-970, Brazil;
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Craig Gutierrez
Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA;
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Caroline Haupt
Interdisciplinary Research Center HALOmem, Institute Biochemistry and Biotechnology, Charles Tan;
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Albert J. R. Heck
Biomolec. Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht;
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Franz Herzog
Gene Center Munich, Dept. Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig Maximilian;
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Lan Huang
Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA;
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Michael R. Hoopmann
Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA;
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Nir Kalisman
Dept. Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus;
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Oleg Klykov
Biomolec. Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht;
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Zdenek Kukacka
Institute of Microbiology, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic;
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Fan Liu
Leibniz Institute of Molecular Pharmacology (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany;
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Michael J. MacCoss
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA;
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Karl Mechtler
Protein Chemistry Facility, Research Institute of Molecular Pathol. (IMP);
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Ravit Mesika
Dept. Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus;
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Robert L. Moritz
Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA;
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Nagarjuna Nagaraj
Biochemistry Core Facility, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martin;
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Victor Nesati
Analytical Biochemistry, CSL Limited, Bio21 Institute, 30 Flemington Road, 3010 Parkville, Australia;
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Robert Ninnis
Analytical Biochemistry, CSL Limited, Bio21 Institute, 30 Flemington Road, 3010 Parkville, Australia;
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Petr Novak
Institute of Microbiology, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic;
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Francis J. O'Reilly
Chair of Bioanalytics, Institute of Biotechnology Technische Universitaet Berlin, Berlin, Germany;
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Matthias Pelzing
Analytical Biochemistry, CSL Limited, Bio21 Institute, 30 Flemington Road, 3010 Parkville, Australia;
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Evgeniy Petrotchenko
University of Victoria -Genome British Columbia Proteomics Centre, Vancouver Island Technology Park;
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Lolita Piersimoni
Depts. Biological Chemistry, Bioinformatics, and Chemistry, University of Michigan, Ann Arbor;
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Manolo Plasencia
Depts. Biological Chemistry, Bioinformatics, and Chemistry, University of Michigan, Ann Arbor;
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Tara Pukala
Discipline of Chemistry, Faculty of Sciences, University of Adelaide, North Terrace, Adelaide;
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Kasper D. Rand
Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark;
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Juri Rappsilber
Chair of Bioanalytics, Institute of Biotechnology Technische Universitaet Berlin, Berlin, Germany;
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Dana Reichmann
Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus;
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Caroline Sailer
University of Konstanz, Department of Biology, Universitaetsstr. 10, 78457 Konstanz, Germany;
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Chris P. Sarnowski
Dept. Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8;
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Richard A. Scheltema
Biomolec. Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research;
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Carla Schmidt
Interdisciplinary Research Center HALOmem, Institute Biochemistry and Biotechnolog;
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David C. Schriemer
Dept. of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, 3330;
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Yi Shi
Department of Cell Biology, University of Pittsburgh, School of Medicine;
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Mark J. Skehel
MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2;
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Moriya Slavin
Dept. Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus;
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Frank Sobott
Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium;
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Victor Solis-Mezarino
Gene Center Munich, Dept. Biochemistry, Faculty of Chemistry and Pharmacy;
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Heike Stephanowitz
Leibniz Institute of Molecular Pharmacology (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany;
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Florian Stengel
University of Konstanz, Department of Biology, Universitaetsstr. 10, 78457 Konstanz, Germany;
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Christian E. Stieger
Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP);
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Michael Trnka
UCSF Mass Spectrometry Facility, Genentech Hall, 600 16th Street, San Francisco, CA 94158, USA;
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Marta Vilaseca
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Tech;
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Rosa Viner
Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA 95134, USA;
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Yufei Xiang
Department of Cell Biology, University of Pittsburgh, School of Medicine;
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Sule Yilmaz
Computational Systems Biochem. Research Group, Max-Planck-Institute of Biochemistry, Am Klopfe;
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Alex Zelter
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Daniel Ziemianowicz
Dept. of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, 3330;
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Alexander Leitner
Dept. Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8;
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Andrea Sinz
Dept. Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Prot;
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  • For correspondence: andrea.sinz@pharmazie.uni-halle.de
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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 largely 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 that are generally accepted in the field and that have shown to lead to high-quality 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. From the results obtained, common protocols will be established. Our study serves as basis for establishing best practice guidelines in the field for conducting cross-linking experiments, performing data analysis, and reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

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Posted September 26, 2018.
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Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines
Claudio Iacobucci, Christine Piotrowski, Ruedi Aebersold, Bruno C. Amaral, Philip Andrews, Christoph Borchers, Nicolas I. Brodie, James E. Bruce, Stephane Chaignepain, Juan D. Chavez, Stephane Claverol, Juergen Cox, Gianluca Degliesposti, Meng Q. Dong, Nufar Edinger, Cecilia Emanuelsson, Marina Gay, Michael Goetze, Fabio C. Gozzo, Craig Gutierrez, Caroline Haupt, Albert J. R. Heck, Franz Herzog, Lan Huang, Michael R. Hoopmann, Nir Kalisman, Oleg Klykov, Zdenek Kukacka, Fan Liu, Michael J. MacCoss, Karl Mechtler, Ravit Mesika, Robert L. Moritz, Nagarjuna Nagaraj, Victor Nesati, Robert Ninnis, Petr Novak, Francis J. O'Reilly, Matthias Pelzing, Evgeniy Petrotchenko, Lolita Piersimoni, Manolo Plasencia, Tara Pukala, Kasper D. Rand, Juri Rappsilber, Dana Reichmann, Caroline Sailer, Chris P. Sarnowski, Richard A. Scheltema, Carla Schmidt, David C. Schriemer, Yi Shi, Mark J. Skehel, Moriya Slavin, Frank Sobott, Victor Solis-Mezarino, Heike Stephanowitz, Florian Stengel, Christian E. Stieger, Michael Trnka, Marta Vilaseca, Rosa Viner, Yufei Xiang, Sule Yilmaz, Alex Zelter, Daniel Ziemianowicz, Alexander Leitner, Andrea Sinz
bioRxiv 424697; doi: https://doi.org/10.1101/424697
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Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines
Claudio Iacobucci, Christine Piotrowski, Ruedi Aebersold, Bruno C. Amaral, Philip Andrews, Christoph Borchers, Nicolas I. Brodie, James E. Bruce, Stephane Chaignepain, Juan D. Chavez, Stephane Claverol, Juergen Cox, Gianluca Degliesposti, Meng Q. Dong, Nufar Edinger, Cecilia Emanuelsson, Marina Gay, Michael Goetze, Fabio C. Gozzo, Craig Gutierrez, Caroline Haupt, Albert J. R. Heck, Franz Herzog, Lan Huang, Michael R. Hoopmann, Nir Kalisman, Oleg Klykov, Zdenek Kukacka, Fan Liu, Michael J. MacCoss, Karl Mechtler, Ravit Mesika, Robert L. Moritz, Nagarjuna Nagaraj, Victor Nesati, Robert Ninnis, Petr Novak, Francis J. O'Reilly, Matthias Pelzing, Evgeniy Petrotchenko, Lolita Piersimoni, Manolo Plasencia, Tara Pukala, Kasper D. Rand, Juri Rappsilber, Dana Reichmann, Caroline Sailer, Chris P. Sarnowski, Richard A. Scheltema, Carla Schmidt, David C. Schriemer, Yi Shi, Mark J. Skehel, Moriya Slavin, Frank Sobott, Victor Solis-Mezarino, Heike Stephanowitz, Florian Stengel, Christian E. Stieger, Michael Trnka, Marta Vilaseca, Rosa Viner, Yufei Xiang, Sule Yilmaz, Alex Zelter, Daniel Ziemianowicz, Alexander Leitner, Andrea Sinz
bioRxiv 424697; doi: https://doi.org/10.1101/424697

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