Systems biology has emerged in the previous decade to provide a holistic study of the biochemical components (genes, transcripts, proteins, and metabolites) and their complex interactions that create the emergent properties or phenotype of biological systems. Metabolomics is a core discipline of systems biology and involves the investigation of low molecular weight organic and inorganic metabolites present in a cell, tissue, organ, or organism.
Metabolomics provides a dynamic and representative phenotypic picture of the system involving endogeneous and exogeneous metabolism and biochemical regulation (e.g., allosterism and riboswitches).
Metabolomic studies are a multistage process involving hypothesis-generation discovery and validation studies. The workflows for experiments and metabolite identification are shown in Figures 1 and 2. Many metabolomics studies start from a point of limited biological knowledge.
A holistic experiment is designed and performed to acquire robust and valid data encompassing a wide and diverse range of metabolites and metabolic pathways. Data is interrogated to define metabolic differences between classes, for example, two classes of subjects diagnosed/not diagnosed with a disease. This strategy is defined as metabolic profiling.