Despite significant advances in analytical methodologies, the comprehensive identification of endogenous and exogenous components within metabolomics datasets remains a formidable challenge. This talk presents three case studies from the Holmes laboratory that illustrate the structural elucidation of complex metabolites encountered during otherwise routine NMR-based metabolomic investigations. The first highlights the structural characterization of trans-3-hexenoyl glutamine (T3HG), a urinary marker associated with mitochondrial overload in children under conditions of severe caloric deprivation. The second describes the discovery of the ddhN series of urinary antiviral biomarkers, capable of distinguishing SARS-CoV-2 infection from healthy controls. The third case details the identification of potassium phosphite in conventionally farmed versus regeneratively grown avocados: a particularly challenging assignment due to the analyte's unusually large spin-spin coupling constant on the order of 600 Hz (approximately 1.5 ppm on a 400 MHz instrument). In each case, structural assignments were supported by advanced NMR and mass spectrometric analyses and, where applicable, confirmed by total synthesis and matrix spiking. Collectively, these studies underscore the value of a multidisciplinary approach to metabolite identification, integrating spectroscopic, chemical, and biological tools to address seemingly intractable analytical problems. The identification and characterization of these metabolites often required extended collaborative efforts spanning months to years, involving data scientists, biologists, analytical chemists, and synthetic chemists. Beyond structure elucidation, the identification of such previously unreported metabolites offers insights into underlying biochemical and physiological processes involved.