The metabolome comprises the complete set of metabolites, the non-genetically encoded substrates, intermediates, and products of metabolic pathways, associated to a cell. By representing integrative information across multiple functional levels and by linking DNA encoded processes with the environment, the metabolome offers a window to map core attributes responsible for different phenotypes. Given increasing demand to quantitatively identify the metabolome and understand how trafficking of metabolites through the metabolic network impact cellular behavior, metabolomics has emerged as an important complementary technology to the cell-wide measurements of mRNA, proteins, fluxes, and interactions (e.g. protein-DNA). Metabolomics is already a powerful tool in drug discovery and development and in metabolic engineering. While maintaining these strengths, the field promises to play a heightened role in systems biology research, which is transforming the practice of medicine and our ability to engineer living organisms.