Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.

Dagmar H Leary, David A Walsh, Nicholas I Symmonds, Adam I Shepherd, Jaclyn K Saunders, Brook L Nunn, Benjamin A Neely, Robert M Morris, Eli K Moore, Matthew R McIlvin, Mak A Saito, Danie B Kinkade, Michael G Janech, Pratik D Jagtap, Robert L Hettich, William Judson Hervey, Noelle A Held, David A Gaylord, Megan E Duffy, Erin M Bertrand

Journal: Journal of proteome research 2020;18(4):1461-1476

PMID: 30702898

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Abstract

Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, colimitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries. Yet challenges remain for ocean metaproteomics due to the great biological diversity that produces highly complex mass spectra, as well as the difficulty in obtaining and working with environmental samples. This review summarizes the progress and challenges facing ocean metaproteomic scientists and proposes best practices for data sharing of ocean metaproteomic data sets, including the data types and metadata needed to enable intercomparisons of protein distributions and annotations that could foster global ocean metaproteomic capabilities.

Address: Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States.; Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada.; School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States.; U.S. Naval Research Laboratory , Washington , D.C. 20375 , United States.; Oak Ridge National Laboratory and Microbiology Department , University of Tennessee , Knoxville , Tennessee 37996 , United States.; Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Saint Paul , Minnesota 55108 , United States.; College of Charleston , Charleston , South Carolina 29424 , United States.; Department of Environmental Science , Rowan University , Glassboro , New Jersey 08028 , United States.; National Institute of Standards and Technology , Charleston , South Carolina 29412 , United States.; Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.; Department of Biology , Concordia University , Montreal , Quebec H4B 1R6 , Canada.

DOI: 10.1021/acs.jproteome.8b00761

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https://doi.org/10.1021/acs.jproteome.8b00761

MeSH Terms: Databases, Protein, Humans, Information Dissemination, Metagenomics, Oceans and Seas, Proteomics, Water Microbiology