Articles | Volume 21, issue 21
https://doi.org/10.5194/bg-21-4889-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-21-4889-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
08 Nov 2024
Research article |
| 08 Nov 2024
| 08 Nov 2024
Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures
Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
Jaclyn K. Saunders
Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
present address: Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
Matthew R. McIlvin
Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
Erin M. Bertrand
Department of Biology, Dalhousie University, Halifax, NS, Canada
John A. Breier
School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, USA
Margaret Mars Brisbin
Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
Sophie M. Colston
Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
Jaimee R. Compton
Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
Tim J. Griffin
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
W. Judson Hervey
Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
Robert L. Hettich
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
Pratik D. Jagtap
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
Michael Janech
Hollings Marine Lab, College of Charleston, Charleston, South Carolina, USA
Rod Johnson
Bermuda Institute of Ocean Sciences, Arizona State University, Bermuda, USA
Rick Keil
School of Oceanography, College of the Environment, University of Washington, Seattle, Washington, USA
Hugo Kleikamp
Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
Dagmar Leary
Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
Lennart Martens
Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
VIB – UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
J. Scott P. McCain
Department of Biology, Dalhousie University, Halifax, NS, Canada
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
Eli Moore
Energy & Minerals (GEM) Science Center, United States Geological Survey, Reston, Virginia, USA
Subina Mehta
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
Dawn M. Moran
Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
Jaqui Neibauer
Hollings Marine Lab, College of Charleston, Charleston, South Carolina, USA
Benjamin A. Neely
Biochemical and Exposure Science Group, National Institute of Standards and Technology, Charleston, South Carolina, USA
Michael V. Jakuba
Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
Jim Johnson
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
deceased
Megan Duffy
Hollings Marine Lab, College of Charleston, Charleston, South Carolina, USA
Gerhard J. Herndl
University of Vienna, Dept. of Functional and Evolutionary Ecology, Vienna, Austria
Richard Giannone
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
Ryan Mueller
Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA
Brook L. Nunn
School of Oceanography, College of the Environment, University of Washington, Seattle, Washington, USA
Martin Pabst
School of Oceanography, College of the Environment, University of Washington, Seattle, Washington, USA
Samantha Peters
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
Andrew Rajczewski
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
Elden Rowland
Department of Biology, Dalhousie University, Halifax, NS, Canada
Brian Searle
Department of Chemistry and Biochemistry, College of Arts and Sciences, Ohio State University, Columbus, Ohio, USA
Tim Van Den Bossche
Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
VIB – UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
Gary J. Vora
Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
Jacob R. Waldbauer
Department of Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
Haiyan Zheng
Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
Zihao Zhao
University of Vienna, Dept. of Functional and Evolutionary Ecology, Vienna, Austria
Data sets
Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures - Submissions from participating laboratories Participants of the Ocean Metaproteome Intercomparison Consortium https://doi.org/10.6019/PXD043218
Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures Matthew McIlvin and Mak Saito https://doi.org/10.6019/PXD044234
Scaffold-derived metaproteomic exclusive and total spectral counts associated with proteins from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019 M. A. Saito and N. Cohen https://doi.org/10.26008/1912/bco-dmo.934706.1
Discrete bottle samples collected at the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea from October 1988 through December 2023 R. J. Johnson et al. https://doi.org/10.26008/1912/bco-dmo.3782.6
Short summary
The ability to assess the functional capabilities of microbes in the environment is of increasing interest. Metaproteomics, the ability to measure proteins across microbial populations, has been increasing in capability and popularity in recent years. Here, an international team of scientists conducted an intercomparison study using samples collected from the North Atlantic Ocean and observed consistency in the peptides and proteins identified, their functions, and their taxonomic origins.
The ability to assess the functional capabilities of microbes in the environment is of...
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