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  • Print publication year: 2018
  • Online publication date: August 2018

22 - Fundamentals of Metabolomics



Metabolomics is essentially the measurement of the thousands of low- molecular-weight metabolites present in a biological system and is an important field of post- genomics biology. Metabolites, and metabolite levels, can be regarded as the physiological end-point of cellular responses to genetic factors, protein expression/activity and environmental changes (for example, nutrient availability). As such, measurement of the metabolite repertoire (or metabolome) of a cell, tissue or biofluid can give a precise snapshot of the physiological state of the system at any given moment (Figure 22.1). Along with its sister ‘-omics’ fields of genomics, transcriptomics and proteomics, metabolomics has important roles in understanding cell biology, but it also has wider-reaching applications, such as in environmental research and toxicology, as well as disease biomarker discovery, drug discovery, drug abuse and forensic science, to name but a few.

As is the case with proteomics (see Chapter 21), metabolomics is not simply one process. In fact, metabolomics encompasses a number of specialised fields, each with their own advantages and challenges, and can range from vast clinical cohort (or population) studies requiring large numbers of samples and deep statistical analysis, to intricate study of flux through specific metabolic pathways in an organelle. Such a wide range of applications requires careful consideration of the approaches required – from experimental design and metabolite extraction techniques to data acquisition and data processing/statistics. However, no matter what approach is taken, sample preparation and choice of data acquisition instrumentation is vital for a successful experiment.


When performing any metabolomics experiment, it is crucial that the samples are prepared in an appropriate fashion. This includes considerations about metabolic quenching, metabolite extraction, sample storage, and preparation of the sample for metabolite analysis (data acquisition).

Metabolic Quenching

One of the key aspects of most metabolomics experiments is the quenching of the metabolism of that cell/tissue/biofluid. Quenching metabolism is the process of halting the metabolic processes of the biosystem as swiftly and reproducibly as possible. This is important for two reasons. Firstly, when we are observing the metabolome of a sample, we wish to view a snap-shot of the metabolism of the system at that precise moment.