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Microbial Metabolomics pp 133–152Cite as

High-Throughput Solid-Phase Microextraction–Liquid Chromatography–Mass Spectrometry for Microbial Untargeted Metabolomics

Part of the Methods in Molecular Biology book series (MIMB,volume 1859)

Abstract

Nowadays, metabolomics data, when combined with other “omics” data, can provide important information regarding systems biology. Acquiring a comprehensive untargeted metabolome snapshot of complex sample matrices requires proper sample preparation, and access to sophisticated analytical instrumentation such as mass spectrometry. In metabolomics, sample preparation has substantial influence on the quality of the obtained metabolome profile. To achieve a real snapshot of the metabolome, the analysis method must be capable of inhibiting metabolite interconversion by immediately quenching all metabolome activity. Application of solid-phase microextraction (SPME), particularly in its in vivo set up, when undertaken in conjunction with a conscious selection of coating type based on the chosen sample matrix and the physicochemical properties of the analytes under study, is capable of providing extraction of representative metabolomes for many biological matrices. Metabolomes identified by SPME include low-abundance species and short-lived or unstable metabolites hardly captured by traditional extraction techniques. SPME coupled to liquid chromatography–high-resolution mass spectrometry has recently been introduced as an innovative alternative technique that integrates sampling, sample preparation, and extraction for metabolic profiling and isolation of candidate biomarkers. This chapter presents a detailed protocol for microbial metabolome analysis of Escherichia coli as a model organism, applying the high-throughput SPME-LC-MS workflow.

Key words

  • High-throughput analysis
  • Metabolomics
  • LC-MS
  • SPME
  • Sample preparation
  • Automation
  • E. coli

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Acknowledgments

The authors thank the Natural Sciences and Engineering Research Council (NSERC) of Canada (IRCPJ 184412-10 050165, IRCPJ 184412-10 050165) for financial support.

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Authors and Affiliations

  1. Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada

    Fatemeh Mousavi

  2. Department of Chemistry, University of Waterloo, Waterloo, Canada

    Barbara Bojko & Janusz Pawliszyn

Authors
  1. Fatemeh Mousavi
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  2. Barbara Bojko
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  3. Janusz Pawliszyn
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Editor information

Editors and Affiliations

  1. Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA

    Ph.D. Edward E.K. Baidoo

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Mousavi, F., Bojko, B., Pawliszyn, J. (2019). High-Throughput Solid-Phase Microextraction–Liquid Chromatography–Mass Spectrometry for Microbial Untargeted Metabolomics. In: Baidoo, E. (eds) Microbial Metabolomics. Methods in Molecular Biology, vol 1859. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8757-3_7

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  • DOI: https://doi.org/10.1007/978-1-4939-8757-3_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8756-6

  • Online ISBN: 978-1-4939-8757-3

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