Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.,Journal of Proteome Research

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Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2019-03-12 , DOI: 10.1021/acs.jproteome.8b00761
Mak A Saito ₁ , Erin M Bertrand ₂ , Megan E Duffy ₃ , David A Gaylord ₁ , Noelle A Held ₁ , William Judson Hervey ₄ , Robert L Hettich ₅ , Pratik D Jagtap ₆ , Michael G Janech ₇ , Danie B Kinkade ₁ , Dagmar H Leary ₄ , Matthew R McIlvin ₁ , Eli K Moore ₈ , Robert M Morris ₃ , Benjamin A Neely ₉ , Brook L Nunn ₁₀ , Jaclyn K Saunders _{1,

3} , Adam I Shepherd ₁ , Nicholas I Symmonds ₁ , David A Walsh ₁₁

Affiliation

Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States.
Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada.
School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States.
U.S. Naval Research Laboratory , Washington , D.C. 20375 , United States.
Oak Ridge National Laboratory and Microbiology Department , University of Tennessee , Knoxville , Tennessee 37996 , United States.
Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Saint Paul , Minnesota 55108 , United States.
College of Charleston , Charleston , South Carolina 29424 , United States.
Department of Environmental Science , Rowan University , Glassboro , New Jersey 08028 , United States.
National Institute of Standards and Technology , Charleston , South Carolina 29412 , United States.
Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.
Department of Biology , Concordia University , Montreal , Quebec H4B 1R6 , 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.

中文翻译：

海洋元蛋白质组学的发展和挑战以及建议的数据共享最佳实践。

海洋元蛋白质组学是一个新兴领域，可以发现海洋微生物群落及其对全球生物地球化学过程的影响。最近的海洋元蛋白质组学研究提供了有关微生物营养物运输，碳固定的局限性，微生物生物膜的代谢以及海洋生态系统中碳通量动态的见解。未来的方法学发展可能会提供新的功能，例如表征长期的生态系统变化，生物地球化学反应速率和原位化学计量。然而，由于巨大的生物多样性会产生高度复杂的质谱图，以及获得和处理环境样品的困难，海洋元蛋白质组学仍然面临挑战。

更新日期：2019-03-13

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