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

Related authors

Zinc stimulation of phytoplankton in a low carbon dioxide, coastal Antarctic environment: evidence for the Zn hypothesis
Riss M. Kell, Adam V. Subhas, Nicole L. Schanke, Lauren E. Lees, Rebecca J. Chmiel, Deepa Rao, Margaret M. Brisbin, Dawn M. Moran, Matthew R. McIlvin, Francesco Bolinesi, Olga Mangoni, Raffaella Casotti, Cecilia Balestra, Tristan Horner, Robert B. Dunbar, Andrew E. Allen, Giacomo R. DiTullio, and Mak A. Saito
EGUsphere, https://doi.org/10.1101/2023.11.05.565706,https://doi.org/10.1101/2023.11.05.565706, 2025
Short summary
Part 2: Quantitative contributions of cyanobacterial alkaline phosphatases to biogeochemical rates in the subtropical North Atlantic
Noelle A. Held, Korrina Kunde, Clare E. Davis, Neil J. Wyatt, Elizabeth L. Mann, E. Malcolm S. Woodward, Matthew McIlvin, Alessandro Tagliabue, Benjamin S. Twining, Claire Mahaffey, Mak A. Saito, and Maeve C. Lohan
EGUsphere, https://doi.org/10.5194/egusphere-2024-3996,https://doi.org/10.5194/egusphere-2024-3996, 2025
Short summary
Part 1: Zonal gradients in phosphorus and nitrogen acquisition and stress revealed by metaproteomes of Prochlorococcus and Synechococcus
Claire Mahaffey, Noelle Held, Korinne Kunde, Clare Davis, Neil Wyatt, Matthew McIlvin, Malcolm Woodward, Lewis Wrightson, Alessandro Tagliabue, Maeve Lohan, and Mak Saito
EGUsphere, https://doi.org/10.5194/egusphere-2024-3987,https://doi.org/10.5194/egusphere-2024-3987, 2025
Short summary
High metabolic zinc demand within native Amundsen and Ross sea phytoplankton communities determined by stable isotope uptake rate measurements
Riss M. Kell, Rebecca J. Chmiel, Deepa Rao, Dawn M. Moran, Matthew R. McIlvin, Tristan J. Horner, Nicole L. Schanke, Ichiko Sugiyama, Robert B. Dunbar, Giacomo R. DiTullio, and Mak A. Saito
Biogeosciences, 21, 5685–5706, https://doi.org/10.5194/bg-21-5685-2024,https://doi.org/10.5194/bg-21-5685-2024, 2024
Short summary
Low cobalt inventories in the Amundsen and Ross seas driven by high demand for labile cobalt uptake among native phytoplankton communities
Rebecca J. Chmiel, Riss M. Kell, Deepa Rao, Dawn M. Moran, Giacomo R. DiTullio, and Mak A. Saito
Biogeosciences, 20, 3997–4027, https://doi.org/10.5194/bg-20-3997-2023,https://doi.org/10.5194/bg-20-3997-2023, 2023
Short summary

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. 
Download
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.
Share
Altmetrics
Final-revised paper
Preprint