The Center for Metabolomics is applying and developing mass spectrometry-based quantitative global analysis of endogenous metabolites from cells, tissues, fluids or whole organisms. While the genome and proteome represent upstream biochemical events, the metabolites correlate with the most downstream biochemistry and therefore most closely represent the phenotype. This has been proven by the broad success of metabolite analysis in clinical diagnostics. The experimental aim in the Center's studies is to obtain a comprehensive quantitative view of the metabolome to expand our understanding of what pathways are altered in specific diseases, what we call "Therapeutic Metabolomics". We have developed multiple novel mass spectrometry platforms for metabolomics including both solution-based approaches and surface-based mass spectrometry, such as nanostructure-initiator mass spectrometry (NIMS) for tissue imaging, to address this problem. These platforms have been applied to diverse areas of chronic pain, cancer, microbial biochemistry, and multiple sclerosis.