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

  • Fatemeh Mousavi
  • Barbara Bojko
  • Janusz Pawliszyn
Part of the Methods in Molecular Biology book series (MIMB, volume 1859)


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 chromatographyhigh-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 



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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Fatemeh Mousavi
    • 1
  • Barbara Bojko
    • 2
  • Janusz Pawliszyn
    • 2
  1. 1.Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
  2. 2.Department of ChemistryUniversity of WaterlooWaterlooCanada

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