Cholesteryl ester (CE) and diacylglycerol (DAG) molecular species are important lipid storage and signaling molecules. Mass spectrometric analyses of these lipids are complicated by the presence of isobaric molecular ions shared by these lipid classes, and by relatively poor electrospray ionization, which is a consequence of an inherent weak dipole moment in these lipid classes. The present study demonstrates that lithiated adducts of CE and DAG molecular ions have enhanced ionization and lipid class specific fragmentation in MS/MS scan modes, thus allowing the implementation of strategies capable of lipid class specific detection. Using neutral loss mode for the loss of cholestane from cholesterol esters (NL 368.5) and specific selected reaction monitoring for DAG molecular species, the response of specific molecular species to that of internal standards was determined. CE and DAG molecular species were quantified in human coronary artery endothelial cells (HCAEC) incubated with both palmitic and oleic acid. Furthermore, NL 368.5 spectra revealed the oxidation of the aliphatic fatty acid residues of cholesterol ester molecular species. Taken together, these studies demonstrate a new analytical approach to assess CE and DAG molecular species that exploits the utility of lithiated adducts in conjunction with MS/MS approaches.