Russo, D.A., Couto, N., Beckerman, A.P. orcid.org/0000-0002-4797-9143 et al. (1 more author) (2019) Metaproteomics of freshwater microbial communities. In: Evans, C.A., Wright, P.C. and Noirel, J., (eds.) Mass Spectrometry of Proteins : Methods and Protocols. Methods in Molecular Biology (1977). Springer Nature , pp. 145-155. ISBN 9781493992317
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.
Metadata
Item Type: | Book Section |
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Authors/Creators: |
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Editors: |
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Copyright, Publisher and Additional Information: | © 2019 Springer Science+Business Media. |
Keywords: | Algae; Bioinformatics; Environmental sample; Functional analysis; Mass spectrometry; Metaproteomics; Microbial community; Protein extraction; Shotgun proteomics; Chromatography, Liquid; Computational Biology; Microbiota; Proteome; Proteomics; Solvents; Tandem Mass Spectrometry; Water Microbiology; Workflow |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Engineering (Sheffield) > Department of Chemical and Biological Engineering (Sheffield) The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) > Department of Animal and Plant Sciences (Sheffield) |
Funding Information: | Funder Grant number Natural Environment Research Council NE/J024767/1 |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 03 Nov 2020 08:04 |
Last Modified: | 03 Nov 2020 08:04 |
Status: | Published |
Publisher: | Springer Nature |
Series Name: | Methods in Molecular Biology |
Refereed: | Yes |
Identification Number: | 10.1007/978-1-4939-9232-4_10 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:167388 |