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4.1 Introduction
Metabolomics is a field which studies the chemically diverse set of biological molecules that are essential components of living systems. These include molecules
such as amino acids, carbohydrates, organic acids, lipids, and nucleotides. The compounds that make up the metabolome typically have molecular weights less than
1800 Da. The metabolites in this mass range are of special interest to the scientific
community due to their dynamic nature and their close relation to phenotype.
Metabolomics differs from its -omic counterparts (genomics, transcriptomics, and
proteomics) in that metabolites are typically the final expression of a complex series
of molecular events that make up system’s biology [1]. Through the study of metabolomics, there is great potential to not only expand our fundamental understanding
of cellular processes, but these discoveries hold the promise to change human
health. The understanding of the end point of disease mechanisms could lead to
improved treatment and detection through the discovery of biomarkers and drug
targets which would improve patient outcomes [2]. As a result, the field of metabolomics research has expanded greatly. Publications have correspondingly increased
exponentially, for example citations related to metabolomics research as increased
665 times from 1992 to 2017 [3].
With this rise in interest, a variety of technologies have been developed and are
currently being applied to the study of metabolites. The principal methods include
NMR (nuclear magnetic resonance) [4], GC-MS/MS (gas chromatography tandem
mass spectrometry) [5], LC-MS/MS (liquid chromatography tandem mass spectrometry) [6], and IMS (imaging mass spectrometry) [7]. NMR-based methods,
which have steadily been increasing for the past 15 years, have a few distinct differences from MS-based platforms: they are largely non-destructive, quantitative, and
require minimal sample preparation (no derivitization, sample treatment or chromatographic separation). However, NMR is 10 to 100 times less sensitive than
LC-MS and GC-MS [8]. Although each method has applications for which it is best
suited, LC-MS and GC-MS methods account for ~80% of all published metabolomics studies. Due to the popularity of these methods, this review will focus primarily on mass spectrometry based methods.
4.1.1 Targeted Vs. Untargeted Assays
In general, metabolic experiments can be characterized by one of two possible
experimental approaches: targeted and untargeted assays (Fig. 4.1). Targeted
approaches probe a specific hypothesis, monitoring a limited number of known
metabolites. Alternatively, untargeted approaches are often used for hypothesis generation and focus on broad coverage of diverse metabolites to identify both known
and unknown metabolic changes.
E. S. Rivera et al.
4.1 Introduction
Metabolomics is a field which studies the chemically diverse set of biological molecules that are essential components of living systems. These include molecules
such as amino acids, carbohydrates, organic acids, lipids, and nucleotides. The compounds that make up the metabolome typically have molecular weights less than
1800 Da. The metabolites in this mass range are of special interest to the scientific
community due to their dynamic nature and their close relation to phenotype.
Metabolomics differs from its -omic counterparts (genomics, transcriptomics, and
proteomics) in that metabolites are typically the final expression of a complex series
of molecular events that make up system’s biology [1]. Through the study of metabolomics, there is great potential to not only expand our fundamental understanding
of cellular processes, but these discoveries hold the promise to change human
health. The understanding of the end point of disease mechanisms could lead to
improved treatment and detection through the discovery of biomarkers and drug
targets which would improve patient outcomes [2]. As a result, the field of metabolomics research has expanded greatly. Publications have correspondingly increased
exponentially, for example citations related to metabolomics research as increased
665 times from 1992 to 2017 [3].
With this rise in interest, a variety of technologies have been developed and are
currently being applied to the study of metabolites. The principal methods include
NMR (nuclear magnetic resonance) [4], GC-MS/MS (gas chromatography tandem
mass spectrometry) [5], LC-MS/MS (liquid chromatography tandem mass spectrometry) [6], and IMS (imaging mass spectrometry) [7]. NMR-based methods,
which have steadily been increasing for the past 15 years, have a few distinct differences from MS-based platforms: they are largely non-destructive, quantitative, and
require minimal sample preparation (no derivitization, sample treatment or chromatographic separation). However, NMR is 10 to 100 times less sensitive than
LC-MS and GC-MS [8]. Although each method has applications for which it is best
suited, LC-MS and GC-MS methods account for ~80% of all published metabolomics studies. Due to the popularity of these methods, this review will focus primarily on mass spectrometry based methods.
4.1.1 Targeted Vs. Untargeted Assays
In general, metabolic experiments can be characterized by one of two possible
experimental approaches: targeted and untargeted assays (Fig. 4.1). Targeted
approaches probe a specific hypothesis, monitoring a limited number of known
metabolites. Alternatively, untargeted approaches are often used for hypothesis generation and focus on broad coverage of diverse metabolites to identify both known
and unknown metabolic changes.
E. S. Rivera et al.