The ability to quantitatively monitor the dynamics of metabolites in an organism is critical to fully understand the complex interactions of biology’s Central Dogma. In part because of the diversity of compounds found in living organisms, especially in plants, the ability to define this critical area in the functional analysis of living plants has been slower to develop than nucleic acid and protein methods. This research addresses impediments to the development of techniques and uses metabolic variations occurring in response to stress conditions as a test system. The present limitations include the rather low numbers of compounds that have typically been identified, relatively insensitive procedures that yield insufficient spatial resolution and the dearth of true quantitative methods. The specific aims are: 1) provide improved sample preparation and derivatization methods that yield structural information to create new spectral library resources for metabolite identification by LC and GC MS, 2) use stable isotope metabolically labeled plant materials for isotope dilution with robust quantification by LC and GC MS and MS/MS, 3) produce temporal and spatial quantitative mapping of metabolites, 4) measure metabolic responses to biotic or abiotic stresses), 5) implement MALDI imaging of fruit at various developmental stages. The work will be focused on rice and tomato, but with the expectation that the methods and procedures will be generally applicable to many plant species.