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

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

doi:10.1021/acs.jproteome.8b00761

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

Journal Article · 30 January 2019 · Journal of Proteome Research

DOI: https://doi.org/10.1021/acs.jproteome.8b00761 · OSTI ID:1509539

^[1]; Bertrand, Erin M. ^[2];

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^[8]; Morris, Robert M. ^[3];

^[9]; Nunn, Brook L. ^[3];

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Woods Hole Oceanographic Inst., Woods Hole, MA (United States)
Dalhousie Univ., Halifax, NS (Canada)
Univ. of Washington, Seattle, WA (United States)
Naval Research Lab. (NRL), Washington, DC (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Univ. of Minnesota, Saint Paul, MN (United States)
College of Charleston, Charleston, SC (United States)
Rowan Univ., Glassboro, NJ (United States)
National Inst. of Standards and Technology (NIST), Charleston, SC (United States)
Woods Hole Oceanographic Inst., Woods Hole, MA (United States); Univ. of Washington, Seattle, WA (United States)
Concordia Univ., Montreal, QC (Canada)

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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1509539

Journal Information:: Journal of Proteome Research, Journal Name: Journal of Proteome Research Journal Issue: 4 Vol. 18; ISSN 1535-3893

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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Additional file 1 of Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics Messer, Lauren F.; Lee, Charlotte E.; Wattiez, Ruddy figshare https://doi.org/10.6084/m9.figshare.25271772.v1	dataset	January 2024
Cyanobacteria and cyanophage contributions to carbon and nitrogen cycling in an oligotrophic oxygen-deficient zone Fuchsman, Clara A.; Palevsky, Hilary I.; Widner, Brittany The ISME Journal, Vol. 13, Issue 11 https://doi.org/10.1038/s41396-019-0452-6	journal	June 2019
Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis Schiebenhoefer, Henning; Van Den Bossche, Tim; Fuchs, Stephan Expert Review of Proteomics, Vol. 16, Issue 5 https://doi.org/10.1080/14789450.2019.1609944	journal	April 2019
Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics Géron, Augustin; Werner, Johannes; Wattiez, Ruddy Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02395	journal	October 2019

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