Metabolomics is facing a major challenge: the lack of knowledge about metabolites present in a given biological system. Thus, large-scale discovery of metabolites is considered an essential step toward a better understanding of plant metabolism. We show here that the application of a metabolomics approach generating structural information for the analysis of Arabidopsis (Arabidopsis thaliana) mutants allows the efficient cataloging of metabolites. Fifty-six percent of the features that showed significant differences in abundance between seeds of wild-type, transparent testa4, and transparent testa5 plants could be annotated. Seventyfive compounds were structurally characterized, 21 of which could be identified. About 40 compounds had not been known from Arabidopsis before. Also, the high-resolution analysis revealed an unanticipated expansion of metabolic conversions upstream of biosynthetic blocks. Deficiency in chalcone synthase results in the increased seed-specific biosynthesis of a range of phenolic choline esters. Similarly, a lack of chalcone isomerase activity leads to the accumulation of various naringenin chalcone derivatives. Furthermore, our data provide insight into the connection between p-coumaroyl-coenzyme A-dependent pathways. Lack of flavonoid biosynthesis results in elevated synthesis not only of p-coumarate-derived choline esters but also of sinapatederived metabolites. However, sinapoylcholine is not the only accumulating end product. Instead, we observed specific and sophisticated changes in the complex pattern of sinapate derivatives.The emergence of metabolomics has for good reasons attracted enormous attention in recent years (Fiehn, 2002;Sumner et al., 2003;Bino et al., 2004). Comprehensive detection of small molecules in a biological system has huge potential as a tool for functional genomics and systems biology. Also, metabolome analysis is expected to contribute significantly to economically important endeavors such as the discovery of bioactive compounds or improving food quality (Dixon et al., 2006;Ryan and Robards, 2006). Currently, however, there is no single analytical approach in sight that would cover the chemical diversity of metabolomes (Dunn and Ellis, 2005), and, perhaps even more problematic, most of the metabolites in any higher eukaryote are as yet unknown (Fernie et al., 2004). Plants in particular synthesize myriad compounds. Plasticity and diversity of metabolism are hallmarks of plant biology, yet we are far from understanding the complex networks of plant metabolism (Last et al., 2007). An essential first step toward a better comprehension of regulation and dynamics is the large-scale discovery of metabolites in Arabidopsis (Arabidopsis thaliana) and other model plants or crops and the cataloging of all of the metabolites that are synthesized in a system under investigation (Last et al., 2007). A large fraction of the thousands of unknowns in any given plant species are secondary metabolites. Fifteen percent to 20% of the genes in Arabidopsis, for instance, are pre...