Liquid chromatography/mass spectrometric methodologies for metabolomics

After the establishment of technologies for high-throughout DNA sequencing (genomics), gene expression analysis (transcriptomics) and protein analysis (proteomics), the remaining challenge for functional genomics is wholesale metabolite analysis---metabolomics. The fundamental role of metabolomics is to correlate relative changes in metabolite levels with functional assignments.; This thesis describes the development of new liquid chromatography-mass spectrometric methodologies for analyzing complex mixtures of analytes with the immediate goal of correlating metabolic and gene expression changes as related to plant defenses. In the process, new internal retention standards were developed for standardizing LC/MS analyses and quantifying metabolites. The unique mass spectrometric fragmentation behavior of a series of phenolic esters was examined as model compounds for secondary plant metabolites. Finally a metabolomics method was established for the analysis of plant extracts by negative mode electrospray ionization mass spectrometry. Quantitative data was collected on over 60 secondary plant metabolites with particular emphasis on plant-insect and plant-pathogen interactions.; The advances described herein will serve to expand the potential of metabolomics and lead the way to fulfilling the goals of functional genomics and systems biology.