Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures
<p>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 com...
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Copernicus Publications
2024-11-01
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| Series: | Biogeosciences |
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| author | 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 |
| author_facet | 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 |
| author_sort | M. A. Saito |
| collection | DOAJ |
| description | <p>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) <i>Clio</i> 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 <span class="inline-formula"><i>R</i><sup>2</sup></span> values averaged <span class="inline-formula">0.62±0.11</span>, 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.</p> |
| format | Article |
| id | doaj-art-bf79b7782bbe4eb8adf50d6e5906b179 |
| institution | Kabale University |
| issn | 1726-4170 1726-4189 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Copernicus Publications |
| record_format | Article |
| series | Biogeosciences |
| spelling | doaj-art-bf79b7782bbe4eb8adf50d6e5906b1792024-11-08T13:56:07ZengCopernicus PublicationsBiogeosciences1726-41701726-41892024-11-01214889490810.5194/bg-21-4889-2024Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis proceduresM. A. Saito0J. K. Saunders1J. K. Saunders2M. R. McIlvin3E. M. Bertrand4J. A. Breier5M. M. Brisbin6S. M. Colston7J. R. Compton8T. J. Griffin9W. J. Hervey10R. L. Hettich11P. D. Jagtap12M. Janech13R. Johnson14R. Keil15H. Kleikamp16D. Leary17L. Martens18L. Martens19J. S. P. McCain20J. S. P. McCain21E. Moore22S. Mehta23D. M. Moran24J. Neibauer25B. A. Neely26M. V. Jakuba27J. Johnson28M. Duffy29G. J. Herndl30R. Giannone31R. Mueller32B. L. Nunn33M. Pabst34S. Peters35A. Rajczewski36E. Rowland37B. Searle38T. Van Den Bossche39T. Van Den Bossche40G. J. Vora41J. R. Waldbauer42H. Zheng43Z. Zhao44Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USAMarine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USApresent address: Department of Marine Sciences, University of Georgia, Athens, Georgia, USAMarine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USADepartment of Biology, Dalhousie University, Halifax, NS, CanadaSchool of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, USAMarine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USACenter for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USACenter for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USACenter for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USABiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USADepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USAHollings Marine Lab, College of Charleston, Charleston, South Carolina, USABermuda Institute of Ocean Sciences, Arizona State University, Bermuda, USASchool of Oceanography, College of the Environment, University of Washington, Seattle, Washington, USADepartment of Biotechnology, Delft University of Technology, Delft, the NetherlandsCenter for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, BelgiumVIB – UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium Department of Biology, Dalhousie University, Halifax, NS, CanadaDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA, USAEnergy & Minerals (GEM) Science Center, United States Geological Survey, Reston, Virginia, USADepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USAMarine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USAHollings Marine Lab, College of Charleston, Charleston, South Carolina, USABiochemical and Exposure Science Group, National Institute of Standards and Technology, Charleston, South Carolina, USAMarine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USADepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USAHollings Marine Lab, College of Charleston, Charleston, South Carolina, USAUniversity of Vienna, Dept. of Functional and Evolutionary Ecology, Vienna, AustriaBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USADepartment of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USASchool of Oceanography, College of the Environment, University of Washington, Seattle, Washington, USASchool of Oceanography, College of the Environment, University of Washington, Seattle, Washington, USABiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USADepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Minneapolis, Minneapolis, Minnesota, USADepartment of Biology, Dalhousie University, Halifax, NS, CanadaDepartment of Chemistry and Biochemistry, College of Arts and Sciences, Ohio State University, Columbus, Ohio, USADepartment of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, BelgiumVIB – UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Geophysical Sciences, University of Chicago, Chicago, Illinois, USACenter for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USAUniversity of Vienna, Dept. of Functional and Evolutionary Ecology, Vienna, Austria<p>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) <i>Clio</i> 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 <span class="inline-formula"><i>R</i><sup>2</sup></span> values averaged <span class="inline-formula">0.62±0.11</span>, 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.</p>https://bg.copernicus.org/articles/21/4889/2024/bg-21-4889-2024.pdf |
| spellingShingle | 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 Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures Biogeosciences |
| title | Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures |
| title_full | Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures |
| title_fullStr | Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures |
| title_full_unstemmed | Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures |
| title_short | Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures |
| title_sort | results from a multi laboratory ocean metaproteomic intercomparison effects of lc ms acquisition and data analysis procedures |
| url | https://bg.copernicus.org/articles/21/4889/2024/bg-21-4889-2024.pdf |
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