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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, Stéphane Chaignepain, Juan D. Chavez, Stéphane Claverol, Jürgen Cox, Gianluca Degliesposti, Meng-Qiu Dong, Nufar Edinger, Cecilia Emanuelsson, Marina Gay, Michael Götze, Fabio C. Gozzo, Craig Gutierrez, Caroline Haupt, Albert J. R. Heck, Franz Herzog, Lan Huang, Michael R. Hoopmann, Nir Kalisman, Oleg Klykov, Zdeněk Kukačka, Fan Liu, Michael J. MacCoss, Karl Mechtler, Ravit Mesika, Robert L. Moritz, Nagarjuna Nagaraj, Victor Nesati, Robert Ninnis, Petr Novák, 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, J. Mark 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
1Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle/Saale, Germany
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Christine Piotrowski
1Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle/Saale, Germany
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Ruedi Aebersold
2Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
3Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
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Bruno C. Amaral
4Institute of Chemistry, University of Campinas, Campinas SP, 13083-970, Brazil
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Philip Andrews
5Departments of Biological Chemistry, Bioinformatics, and Chemistry, University of Michigan, Ann Arbor Michigan, USA
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Christoph Borchers
6University of Victoria -Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
7Department of Biochemistry and Microbiology, University of Victoria, Petch Building, Room 270d, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
8Gerald Bronfman Department of Oncology, Jewish General Hospital and McGill University, 3755 Côte Ste-Catherine Road, Montréal, Quebec H3T 1E2, Canada
9Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montréal, Quebec H3T 1E2, Canada
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Nicolas I. Brodie
6University of Victoria -Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
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James E. Bruce
10Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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Stéphane Chaignepain
11CBMN, UMR 5248, CNRS, Université de Bordeaux, INP Bordeaux, Pessac, France
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Juan D. Chavez
10Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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Stéphane Claverol
12Centre de Génomique Fonctionnelle, Plateforme Protéome, Université de Bordeaux, Bordeaux, France
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Jürgen Cox
13Computational Systems Biochemistry Research Group, Max-Planck-lnstitute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Gianluca Degliesposti
14MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Cambridge CB2 0QH, UK
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Meng-Qiu Dong
15National Institute of Biological Sciences, Beijing, 7 Science Park Road, ZGC Life Science Park, 102206 Beijing, China
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Nufar Edinger
16Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Cecilia Emanuelsson
17Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 22100 Lund, Sweden
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Marina Gay
18Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
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Michael Götze
19Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle/Saale, Germany
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Fabio C. Gozzo
4Institute of Chemistry, University of Campinas, Campinas SP, 13083-970, Brazil
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Craig Gutierrez
20Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA
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Caroline Haupt
21Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle/Saale, Germany
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Albert J. R. Heck
22Biomolecular 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
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Franz Herzog
23Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig Maximilians University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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Lan Huang
20Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA
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Michael R. Hoopmann
24Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
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Nir Kalisman
16Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Oleg Klykov
22Biomolecular 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
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Zdeněk Kukačka
25Institute of Microbiology, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
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Fan Liu
26Leibniz Institute of Molecular Pharmacology (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
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Michael J. MacCoss
27Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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Karl Mechtler
28Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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Ravit Mesika
16Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Robert L. Moritz
24Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
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Nagarjuna Nagaraj
29Biochemistry Core Facility, Max-Planck-lnstitute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Victor Nesati
30Analytical Biochemistry, CSL Limited, Bio21 Institute, 30 Flemington Road, 3010 Parkville, Australia
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Robert Ninnis
30Analytical Biochemistry, CSL Limited, Bio21 Institute, 30 Flemington Road, 3010 Parkville, Australia
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Petr Novák
25Institute of Microbiology, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
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Francis J O’Reilly
31Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin, Berlin, Germany
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Matthias Pelzing
30Analytical Biochemistry, CSL Limited, Bio21 Institute, 30 Flemington Road, 3010 Parkville, Australia
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Evgeniy Petrotchenko
6University of Victoria -Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
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Lolita Piersimoni
5Departments of Biological Chemistry, Bioinformatics, and Chemistry, University of Michigan, Ann Arbor Michigan, USA
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Manolo Plasencia
5Departments of Biological Chemistry, Bioinformatics, and Chemistry, University of Michigan, Ann Arbor Michigan, USA
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Tara Pukala
32Discipline of Chemistry, Faculty of Sciences, University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia
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Kasper D. Rand
33Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
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Juri Rappsilber
31Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin, Berlin, Germany
34Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Dana Reichmann
16Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Caroline Sailer
35University of Konstanz, Department of Biology, Universitätsstr. 10, 78457 Konstanz, Germany
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Chris P. Sarnowski
2Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
36PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland
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Richard A. Scheltema
22Biomolecular 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
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Carla Schmidt
21Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle/Saale, Germany
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David C. Schriemer
37Dept. of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, 3330 Hospital Dr. NW, Calgary, Alberta T2N 4N1, Canada
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Yi Shi
40Department of Cell Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
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J. Mark Skehel
14MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Cambridge CB2 0QH, UK
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Moriya Slavin
16Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Frank Sobott
42Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
43The Astbury Centre for Structural Molecular Biology, and ⍰School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
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Victor Solis-Mezarino
23Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig Maximilians University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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Heike Stephanowitz
26Leibniz Institute of Molecular Pharmacology (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
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Florian Stengel
35University of Konstanz, Department of Biology, Universitätsstr. 10, 78457 Konstanz, Germany
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Christian E. Stieger
28Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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Michael Trnka
38UCSF Mass Spectrometry Facility, Genentech Hall, 600 16th Street, San Francisco, CA 94158, USA
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Marta Vilaseca
18Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
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Rosa Viner
39Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA 95134, USA
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Yufei Xiang
40Department of Cell Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
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Sule Yilmaz
13Computational Systems Biochemistry Research Group, Max-Planck-lnstitute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Alex Zelter
41Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Daniel Ziemianowicz
37Dept. of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, 3330 Hospital Dr. NW, Calgary, Alberta T2N 4N1, Canada
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Alexander Leitner
2Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
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Andrea Sinz
1Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle/Saale, Germany
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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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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, Stéphane Chaignepain, Juan D. Chavez, Stéphane Claverol, Jürgen Cox, Gianluca Degliesposti, Meng-Qiu Dong, Nufar Edinger, Cecilia Emanuelsson, Marina Gay, Michael Götze, Fabio C. Gozzo, Craig Gutierrez, Caroline Haupt, Albert J. R. Heck, Franz Herzog, Lan Huang, Michael R. Hoopmann, Nir Kalisman, Oleg Klykov, Zdeněk Kukačka, Fan Liu, Michael J. MacCoss, Karl Mechtler, Ravit Mesika, Robert L. Moritz, Nagarjuna Nagaraj, Victor Nesati, Robert Ninnis, Petr Novák, 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, J. Mark 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, Stéphane Chaignepain, Juan D. Chavez, Stéphane Claverol, Jürgen Cox, Gianluca Degliesposti, Meng-Qiu Dong, Nufar Edinger, Cecilia Emanuelsson, Marina Gay, Michael Götze, Fabio C. Gozzo, Craig Gutierrez, Caroline Haupt, Albert J. R. Heck, Franz Herzog, Lan Huang, Michael R. Hoopmann, Nir Kalisman, Oleg Klykov, Zdeněk Kukačka, Fan Liu, Michael J. MacCoss, Karl Mechtler, Ravit Mesika, Robert L. Moritz, Nagarjuna Nagaraj, Victor Nesati, Robert Ninnis, Petr Novák, 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, J. Mark 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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