Here, we report a new epoxidation workflow that contributes to these ongoing efforts to fully characterize lipid structures in lipidomics studies. The epoxidation method relies on the photochemical reaction of unsaturated lipids in a flow reactor to form epoxides with 60 -80 % apparent reaction yield. Whereas the formed epoxides can reveal DB position, we describe the capabilities to also identify sn-isomers based on MS n experiments. In addition to DB position and sn-isomer discrimination capabilities, the reported workflows allow improved separation of epoxidized lipids by RPLC compared to non-reacted lipids as well as the identification of E/Z isomers of DBs by comparing RPLC profiles of non-reacted lipids before and after the epoxidation procedure. To demonstrate the capabilities of the method for shotgun and LC-MS lipidomics workflows, we identified DB positions of PCs, PEs, PSs, DGs, TGs in complex polar lipid extracts and revealed 56 sn-isomers in HeLa and H9c2 cell extracts.