Plants are amazing synthetic chemists that create diversified secondary metabolites which play myriad ecological roles for their survival and reproductive fitness in nature. The structural complexity of secondary metabolism has severely hampered its functional analysis. The potential of MS-based metabolomics and of the large-scale acquisition of tandem MS (MS/MS) spectra is limited by the absence of straightforward classification and visualization pipelines so that secondary metabolite and the underlying pathway interpretations can be easily made. From a mechanistic standpoint, secondary metabolism diversity attributes to the occurrence of multiplicity of genes in plant genomes. Yet the majorities of metabolic gene functions remain however unknown. In this thesis, I developed a workflow to systematically explore the diversity of secondary metabolism in Nicotiana attenuata – a metabolically rich ecological model plant. I first characterize the metabolic space of this model plant using the large-scale acquisition of MS/MS spectral information in a data-independent manner and the computational re-assembly of non-redundant MS/MS spectra. The resulting MS signatures were then aligned and visualized to rapidly formulate structural hypotheses. Using natural variation, I examined the correlations among jasmonate signaling and large-scale defense metabolism. The resulting correlation maps uncovered new metabolic layers in a plant’s jasmonate-mediated defensive arsenal. In the tissue-level exploration of secondary metabolite diversity, Transciptomic and metabolomic information and their variance as analyzed by information theory were used for the predictions of tissue-specific function of genes responsible for the metabolic signatures.