Articles | Volume 21, issue 21
https://doi.org/10.5194/bg-21-4889-2024
https://doi.org/10.5194/bg-21-4889-2024
Research article
 | 
08 Nov 2024
Research article |  | 08 Nov 2024

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Mak A. Saito, Jaclyn K. Saunders, Matthew R. McIlvin, Erin M. Bertrand, John A. Breier, Margaret Mars Brisbin, Sophie M. Colston, Jaimee R. Compton, Tim J. Griffin, W. Judson Hervey, Robert L. Hettich, Pratik D. Jagtap, Michael Janech, Rod Johnson, Rick Keil, Hugo Kleikamp, Dagmar Leary, Lennart Martens, J. Scott P. McCain, Eli Moore, Subina Mehta, Dawn M. Moran, Jaqui Neibauer, Benjamin A. Neely, Michael V. Jakuba, Jim Johnson, Megan Duffy, Gerhard J. Herndl, Richard Giannone, Ryan Mueller, Brook L. Nunn, Martin Pabst, Samantha Peters, Andrew Rajczewski, Elden Rowland, Brian Searle, Tim Van Den Bossche, Gary J. Vora, Jacob R. Waldbauer, Haiyan Zheng, and Zihao Zhao

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Cited articles

Bender, S. J., Moran, D. M., McIlvin, M. R., Zheng, H., McCrow, J. P., Badger, J., DiTullio, G. R., Allen, A. E., and Saito, M. A.: Colony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistry, Biogeosciences, 15, 4923–4942, https://doi.org/10.5194/bg-15-4923-2018, 2018. 
Bergauer, K., Fernandez-Guerra, A., Garcia, J. A., Sprenger, R. R., Stepanauskas, R., Pachiadaki, M. G., Jensen, O. N., and Herndl, G. J.: Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics, P. Natl. Acad. Sci. USA, 115, E400–E408, https://doi.org/10.1073/pnas.1708779115, 2018. 
Bertrand, E. M., Moran, D. M., McIlvin, M. R., Hoffman, J. M., Allen, A. E., and Saito, M. A.: Methionine synthase interreplacement in diatom cultures and communities: Implications for the persistence of B12 use by eukaryotic phytoplankton, Limnol. Oceanogr., 58, 1431–1450, 2013. 
Breier, J. A., Jakuba, M. V., Saito, M. A., Dick, G. J., Grim, S. L., Chan, E. W., McIlvin, M. R., Moran, D. M., Alanis, B. A., and Allen, A. E.: Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle, Science Robotics, 5, eabc7104, https://doi.org/10.1126/scirobotics.abc7104, 2020. 
Buchfink, B., Xie, C., and Huson, D. H.: Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59–60, 2015. 
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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.
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