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

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

Research output: Contribution to journalReview articlepeer-review

18 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1461-1476
Number of pages16
JournalJournal of Proteome Research
Volume18
Issue number4
DOIs
StatePublished - Apr 5 2019

Bibliographical note

Funding Information:
The workshop that led to this manuscript was funded by an NSF EarthCube Grant No. 1639714, the Gordon and Betty Moor Foundation, and an anonymous donor to M.A.S. and D.K. We thank Mary Zawoysky for assistance with workshop planning and manuscript editing, two anonymous reviewers for their useful comments and suggestions, and Natalie Renier for graphics assistance.

Keywords

  • Metaproteomics
  • best practices
  • biogeochemistry
  • data sharing
  • ocean

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