This paper describes the surplus value of a quadrupole-orthogonal acceleration TOF mass spectrometer, coupled to a liquid chromatographic separation system, for the unequivocal identification and structural elucidation of an unknown compound in the field of designer drugs. In a patient sample set (blood, tissues, vitreous humor, etc.), analyzed with a dedicated liquid chromatographic-fluorescence detection method for the determination of methylenedioxy amphetamine, methylenedioxy methamphetamine, and methylenedioxy ethylamphetamine (MDEA), a "strange" inexplicable peak appeared at a retention time not corresponding to any of our reference materials. Based on the identical excitation and emission wavelengths in detection, and a retention behavior comparable to MDEA, it was assumed that this unknown compound was an isomer of the recreational drug MDEA. With a simple and straightforward methodological crossover between LC fluorescence detection and LC-MS/MS, additional information for structural elucidation was easily obtained. Chromatographic separation was achieved on a Hypersil BDS C18 column (fluorescence detection part) and on a Hypersil BDS phenyl column (mass spectrometric detection part). MS showed that the unknown compound's molecular mass was identical to that of MDEA, and, in addition, its fragmentation pattern too proved quite similar to that of MDEA. A thorough literature overview and study of the fragmentation pattern by means of the MS/MS spectrum led to an evidence-based hypothesis of 3,4-methylenedioxy N,N-dimethylamphetamine (MDDM) being the unknown compound. To confirm this hypothesis, MDDM was synthesized and its presence in our biological sample was finally demonstrated by co-injection with alternatively synthesized MDDM and MDEA. This application shows the synergism between LC and MS in the elucidation of unknown compounds, nevertheless emphasizing the essence of chromatographic separation when dealing with isomers.