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

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.

Authors:
ORCiD logo [1];  [2]; ORCiD logo [3]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [6]; ORCiD logo [7]; ORCiD logo [1]; ORCiD logo [4]; ORCiD logo [1]; ORCiD logo [8];  [3]; ORCiD logo [9];  [3]; ORCiD logo [10]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [11]
  1. Woods Hole Oceanographic Inst., Woods Hole, MA (United States)
  2. Dalhousie Univ., Halifax, NS (Canada)
  3. Univ. of Washington, Seattle, WA (United States)
  4. Naval Research Lab. (NRL), Washington, DC (United States)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  6. Univ. of Minnesota, Saint Paul, MN (United States)
  7. College of Charleston, Charleston, SC (United States)
  8. Rowan Univ., Glassboro, NJ (United States)
  9. National Inst. of Standards and Technology (NIST), Charleston, SC (United States)
  10. Woods Hole Oceanographic Inst., Woods Hole, MA (United States); Univ. of Washington, Seattle, WA (United States)
  11. Concordia Univ., Montreal, QC (Canada)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1509539
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Proteome Research
Additional Journal Information:
Journal Volume: 18; Journal Issue: 4; Journal ID: ISSN 1535-3893
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES

Citation Formats

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., and Walsh, David A.. Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. United States: N. p., 2019. Web. 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. United States. 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., and Walsh, David A.. Thu . "Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing". United States. https://doi.org/10.1021/acs.jproteome.8b00761. https://www.osti.gov/servlets/purl/1509539.
@article{osti_1509539,
title = {Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing},
author = {Saito, Mak A. and Bertrand, Erin M. and Duffy, Megan E. and Gaylord, David A. and Held, Noelle A. and Hervey, William Judson and Hettich, Robert L. and Jagtap, Pratik D. and Janech, Michael G. and Kinkade, Danie B. and Leary, Dagmar H. and McIlvin, Matthew R. and Moore, Eli K. and Morris, Robert M. and Neely, Benjamin A. and Nunn, Brook L. and Saunders, Jaclyn K. and Shepherd, Adam I. and Symmonds, Nicholas I. and Walsh, David A.},
abstractNote = {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.},
doi = {10.1021/acs.jproteome.8b00761},
journal = {Journal of Proteome Research},
number = 4,
volume = 18,
place = {United States},
year = {2019},
month = {1}
}

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    Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis
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