An extensive comparative study on the electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) mass spectrometry using automated flow injection analysis (FIA), was performed on eurycomanone ( 1), 13 α(21)-epoxyeurycomanone ( 2), eurycomanol ( 3), eurycomanol-2- O- β- d-glucopyranoside ( 4), and 13,21-dihydroeurycomanone ( 5), the bioactive markers isolated from Eurycoma longifolia. The effects of eluent mixture (methanol or acetonitrile in water) and acidic modifiers (acetic acid, formic acid and trifluoroacetic acid) on the ionization efficiency of the markers were also investigated. The ESI in the positive ion mode with methanol containing 0.1% (v/v) acetic acid was selected for the subsequent optimization of nebulizer pressure, dry gas flow, dry gas temperature and capillary voltage to improve the sensitivity of the total ion chromatogram (TIC). Fragmentation of the analytes was further investigated by varying the capillary exit offset voltage and fragmentation amplitude in positive mode of ESI. The detection limits (LODs) were determined in isolation mode (selected ion monitoring, SIM). Their limits of detection (LODs) ranged between 0.03 and 0.1 μg mL −1 while the intra-day and inter-day precisions were less than 5.72% and 4.82%, respectively. The method was next applied for the simultaneous analysis of the markers to standardize various batches of manufactured extracts of E. longifolia for potential use as antimalarial products. Multiple Reaction Monitoring (MRM) mode was used for the quantification of analytes which gave protonated molecular ion, [M+H] +. For those without pseudo-molecular ions, SIM mode was used to quantify the analytes. The batches contained 5.65–9.95% of eurycomanone ( 1), 5.21–19.75% of eurycomanol ( 3) and 7.59–19.95% of eurycomanol-2- O- β- d-glucopyranoside ( 4) as major quassinoids whereas, 13 α(21)-epoxyeurycomanone ( 2), and 13,21-dihydroeurycomanone ( 5) were much lower in concentrations of 0.78–3.90% and 0.47–1.76%, respectively.
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