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This thesis presents efforts to improve the methodology of matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) as a method for analysis of metabolites from plant tissue samples. The first chapter consists of a general introduction to the technique of MALDI-MSI, and the sixth and final chapter provides a brief summary and an outlook on future work. The second chapter (following a general introduction) illustrates how MALDI-MSI of metabolites can be combined with genomics knowledge to infer functional genomic information. Wild-type Arabidopsis flower petals were investigated for their content of three flavonoids (kaempferol, quercetin, and isorhamnetin) and their glucosides, and compared to a well-understood flavonoid mutant (tt7). Spatially non-uniform accumulation/depletion of flavonoids is observed between the wild-type and mutant, and metabolite abundances are compared to infer information about localized gene expression. The third chapter demonstrates a novel small molecule application for a matrix previously used for MALDI-MSI of lipids (1,5-diaminonaphthalene, DAN). DAN was compared to other common MALDI matrices for its efficiency in ionization of several plant metabolite standards, and was found to be comparable or superior for all tested metabolites. DAN was then applied to image a range of classes of metabolites from a crosssection of corn leaf. The fourth chapter presents a novel acquisition method, in which high-mass resolution and tandem MS scans are acquired in alternating polarities during a single

Development of matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) for plant metabolite analysis