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

doi:10.1021/acs.jproteome.8b00761

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:

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

^[3];

^[1];

^[4];

^[5];

^[6];

^[7];

^[1];

^[4];

^[1];

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

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

^[10];

^[1];

^[11]

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)

Publication Date:: 2019-01-31

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

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

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                    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.  doi:10.1021/acs.jproteome.8b00761.  https://www.osti.gov/servlets/purl/1509539.

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@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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DOI: 10.1021/acs.jproteome.8b00761

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Similar Records

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

Abstract

Citation Formats

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Cyanobacteria and cyanophage contributions to carbon and nitrogen cycling in an oligotrophic oxygen-deficient zone journal, June 2019

Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis journal, April 2019

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journal, June 2019

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journal, June 2019

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journal, April 2019

Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
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