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Mass Spectrometry of Proteins pp 145–155Cite as

Metaproteomics of Freshwater Microbial Communities

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1977))

Abstract

Recent advances in metaproteomics have provided us a link between genomic expression and functional characterization of environmental microbial communities. Therefore, the large-scale identification of proteins expressed by environmental microbiomes allows an unprecedented view of their in situ metabolism and function. However, one of the main challenges in metaproteomics remains the lack of robust analytical pipelines. This is especially true for aquatic environments with low protein concentrations and the presence of compounds that are known to interfere with traditional sample preparation pipelines and downstream LC-MS/MS analyses. In this chapter, a semiquantitative method that spans from sample preparation to functional annotation is provided. This method has been shown to provide in-depth and representative results of both the eukaryotic and prokaryotic fractions of freshwater microbiomes.

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Acknowledgments

The authors would like to thank the Natural Environment Research Council (NE/J024767/1) and the Technology Strategy Board for funding this work.

Author information

Authors and Affiliations

  1. Department of Plant and Environmental Sciences, University of Copenhagan, Copenhagan, Denmark

    David A. Russo

  2. Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK

    Narciso Couto & Jagroop Pandhal

  3. Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, UK

    Andrew P. Beckerman

Authors
  1. David A. Russo
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  2. Narciso Couto
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  3. Andrew P. Beckerman
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  4. Jagroop Pandhal
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Corresponding author

Correspondence to Jagroop Pandhal .

Editor information

Editors and Affiliations

  1. Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, South Yorkshire, UK

    Caroline A. Evans

  2. Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, UK

    Phillip C. Wright

  3. Laboratoire GBCM (EA4627), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France

    Josselin Noirel

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Russo, D.A., Couto, N., Beckerman, A.P., Pandhal, J. (2019). Metaproteomics of Freshwater Microbial Communities. In: Evans, C., Wright, P., Noirel, J. (eds) Mass Spectrometry of Proteins. Methods in Molecular Biology, vol 1977. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9232-4_10

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  • DOI: https://doi.org/10.1007/978-1-4939-9232-4_10

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9231-7

  • Online ISBN: 978-1-4939-9232-4

  • eBook Packages: Springer Protocols

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