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Secoiridoids play a key role in determining health benefits related to a regular consumption of extra-virgin olive oil (EVOO), in which they are generated from precursors of the same class naturally occurring in drupes and leaves of the olive (<i>Olea europaea</i> L.) plant. Here, reversed-phase liquid chromatography coupled to electrospray ionization and Fourier-transform single/tandem mass spectrometry (RPLC-ESI-FTMS and MS/MS) was employed for a structural elucidation of those precursors. The presence of three isoforms in both matrices was assessed for oleuropein ([M-H]⁻ ion with <i>m</i>/<i>z</i> 539.1770) and was emphasized, for the first time, also for ligstroside (<i>m</i>/<i>z</i> 523.1821) and for the demethylated counterparts of the two compounds (<i>m</i>/<i>z</i> 525.1614 and 509.1665, respectively). However, only the prevailing isoform included an exocyclic double bond between carbon atoms C⁸ and C⁹, typical of oleuropein and ligstroside; the remaining, less abundant, isoforms included a C=C bond between C⁸ and C¹⁰. The same structural difference was also observed between secoiridoids named elenolic acid glucoside and secoxyloganin (<i>m</i>/<i>z</i> 403.1246). This study strengthens the hypothesis that secoiridoids including a C⁸=C¹⁰ bond, recently recognized as relevant species in EVOO extracts, arise mainly from specific enzymatic/chemical transformations occurring on major oleuropein/ligstroside-like precursors during EVOO production, rather than from precursors having that structural feature.