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 article

2 Citations (Scopus)

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

Fingerprint

Information Dissemination
Practice Guidelines
Oceans and Seas
Carbon
Aquatic ecosystems
Biodiversity
Biofilms
Metadata
Metabolism
Stoichiometry
Ecosystems
Nutrients
Reaction rates
Carbon Cycle
Fluxes
Ecosystem
Molecular Sequence Annotation
Proteins
Food

Keywords

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

PubMed: MeSH publication types

  • Journal Article

Cite this

Saito, M. A., Bertrand, E. M., Duffy, M. E., Gaylord, D. A., Held, N. A., Hervey, W. J., ... Walsh, D. A. (2019). Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. Journal of Proteome Research, 18(4), 1461-1476. https://doi.org/10.1021/acs.jproteome.8b00761

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.

In: Journal of Proteome Research, Vol. 18, No. 4, 05.04.2019, p. 1461-1476.

Research output: Contribution to journalReview article

Saito, MA, Bertrand, EM, Duffy, ME, Gaylord, DA, Held, NA, Hervey, WJ, Hettich, RL, Jagtap, PD, Janech, MG, Kinkade, DB, Leary, DH, McIlvin, MR, Moore, EK, Morris, RM, Neely, BA, Nunn, BL, Saunders, JK, Shepherd, AI, Symmonds, NI & Walsh, DA 2019, 'Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing', Journal of Proteome Research, vol. 18, no. 4, pp. 1461-1476. https://doi.org/10.1021/acs.jproteome.8b00761
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. / Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. In: Journal of Proteome Research. 2019 ; Vol. 18, No. 4. pp. 1461-1476.
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