Abstract
Metabolites are small molecules produced by enzymatic reactions in a given organism. Metabolomics or metabolic phenotyping is a well-established omics aimed at comprehensively assessing metabolites in biological systems. These comprehensive analyses use analytical platforms, mainly nuclear magnetic resonance spectroscopy and mass spectrometry, along with associated separation methods to gather qualitative and quantitative data. Metabolomics holistically evaluates biological systems in an unbiased, data-driven approach that may ultimately support generation of hypotheses. The approach inherently allows the molecular characterization of a biological sample with regard to both internal (genetics) and environmental (exosome, microbiome) influences. Metabolomics workflows are based on whether the investigator knows a priori what kind of metabolites to assess. Thus, a targeted metabolomics approach is defined as a quantitative analysis (absolute concentrations are determined) or a semiquantitative analysis (relative intensities are determined) of a set of metabolites that are possibly linked to common chemical classes or a selected metabolic pathway. An untargeted metabolomics approach is a semiquantitative analysis of the largest possible number of metabolites contained in a biological sample. This is part I of a review intending to give an overview of the state of the art of major metabolic phenotyping technologies. Furthermore, their inherent analytical advantages and limits regarding experimental design, sample handling, standardization and workflow challenges are discussed.
Highlights
Systems biology is a new scientific paradigm aimed at unveiling the systemic function of biology and bridging the gap between biological information and its context
Metabolomics has its roots in the practices of ancient Greek doctors who used the organoleptic characteristics of urine for diagnosis; for example, urine sweetness reveals the high glucose levels in diabetes
For more details on metabolomics potential in inherited metabolic diseases (IMD), the reader may refer to recent comprehensive reviews (Piras et al 2016; Tebani et al 2016a, b)
Summary
Systems biology is a new scientific paradigm aimed at unveiling the systemic function of biology and bridging the gap between biological information and its context. These techniques permit direct sampling of complex matrices under ambient conditions, and they include atmospheric solids analysis probe (Twohig et al 2010), desorption electrospray ionization (Eberlin et al 2013; Ferreira et al 2015; Kerian et al 2015), and rapid evaporative ionization MS methods (Balog et al 2013; Balog et al 2015) These techniques can provide real-time, interpretable MS data on biofluids and tissues, in vivo and ex vivo, and they are reshaping high-throughput real-time metabolome analysis in different areas (Arentz et al 2017; Dunham et al 2017). Data integrity and analytical quality assessment is tightly regulated and different guidelines have been issued by regulatory bodies regarding bioanalytical method validation criteria (Kadian et al 2016) These criteria may include accuracy, precision, specificity, limit of detection, limit of quantitation, and linearity. Inspecting the distribution of the R2 values may help in setting
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