Biogeosciences (Nov 2024)
Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures
- M. A. Saito,
- J. K. Saunders,
- J. K. Saunders,
- M. R. McIlvin,
- E. M. Bertrand,
- J. A. Breier,
- M. M. Brisbin,
- S. M. Colston,
- J. R. Compton,
- T. J. Griffin,
- W. J. Hervey,
- R. L. Hettich,
- P. D. Jagtap,
- M. Janech,
- R. Johnson,
- R. Keil,
- H. Kleikamp,
- D. Leary,
- L. Martens,
- L. Martens,
- J. S. P. McCain,
- J. S. P. McCain,
- E. Moore,
- S. Mehta,
- D. M. Moran,
- J. Neibauer,
- B. A. Neely,
- M. V. Jakuba,
- J. Johnson,
- M. Duffy,
- G. J. Herndl,
- R. Giannone,
- R. Mueller,
- B. L. Nunn,
- M. Pabst,
- S. Peters,
- A. Rajczewski,
- E. Rowland,
- B. Searle,
- T. Van Den Bossche,
- T. Van Den Bossche,
- G. J. Vora,
- J. R. Waldbauer,
- H. Zheng,
- Z. Zhao
Affiliations
- M. A. Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- J. K. Saunders
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- J. K. Saunders
- present address: Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- M. R. McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- E. M. Bertrand
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- J. A. Breier
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, USA
- M. M. Brisbin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- S. M. Colston
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
- J. R. Compton
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
- T. J. Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
- W. J. Hervey
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
- R. L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- P. D. Jagtap
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
- M. Janech
- Hollings Marine Lab, College of Charleston, Charleston, South Carolina, USA
- R. Johnson
- Bermuda Institute of Ocean Sciences, Arizona State University, Bermuda, USA
- R. Keil
- School of Oceanography, College of the Environment, University of Washington, Seattle, Washington, USA
- H. Kleikamp
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
- D. Leary
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
- L. Martens
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
- L. Martens
- VIB – UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- J. S. P. McCain
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- J. S. P. McCain
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- E. Moore
- Energy & Minerals (GEM) Science Center, United States Geological Survey, Reston, Virginia, USA
- S. Mehta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
- D. M. Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- J. Neibauer
- Hollings Marine Lab, College of Charleston, Charleston, South Carolina, USA
- B. A. Neely
- Biochemical and Exposure Science Group, National Institute of Standards and Technology, Charleston, South Carolina, USA
- M. V. Jakuba
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- J. Johnson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
- M. Duffy
- Hollings Marine Lab, College of Charleston, Charleston, South Carolina, USA
- G. J. Herndl
- University of Vienna, Dept. of Functional and Evolutionary Ecology, Vienna, Austria
- R. Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- R. Mueller
- Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA
- B. L. Nunn
- School of Oceanography, College of the Environment, University of Washington, Seattle, Washington, USA
- M. Pabst
- School of Oceanography, College of the Environment, University of Washington, Seattle, Washington, USA
- S. Peters
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- A. Rajczewski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USA
- E. Rowland
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- B. Searle
- Department of Chemistry and Biochemistry, College of Arts and Sciences, Ohio State University, Columbus, Ohio, USA
- T. Van Den Bossche
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
- T. Van Den Bossche
- VIB – UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- G. J. Vora
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
- J. R. Waldbauer
- Department of Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
- H. Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
- Z. Zhao
- University of Vienna, Dept. of Functional and Evolutionary Ecology, Vienna, Austria
- DOI
- https://doi.org/10.5194/bg-21-4889-2024
- Journal volume & issue
-
Vol. 21
pp. 4889 – 4908
Abstract
Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.
