Extracts of Eurycoma longifolia Jack (EL) and Eurycoma harmandiana Pierre (EH) contain numerous bioactive compounds and varying matrices that are challenging to separate using chromatographic techniques. Herein, micellar liquid chromatography (MLC) was used to analyze canthin-6-one alkaloids contained in these extracts, and the achieved performance was compared with that of a conventional high-performance liquid chromatography (HPLC) method. The optimal mobile phase of MLC corresponded to 15 : 85 (v/v) acetonitrile : water (pH 3) containing 110 mM sodium dodecyl sulfate and 10 mM NaH2PO4. The retention times of canthin-6-one-9-O-β-d-glucopyranoside, 9-hydroxycanthin-6-one, canthin-6-one, and 9-methoxycanthin-6-one were 4.78/15.42, 17.64/24.11, 32.84/38.27, and 39.04/39.86 min, respectively, in the cases of isocratic MLC and conventional HPLC. In both cases, the analyte resolution exceeded 1.5. The MLC elution behavior of the examined analytes was largely determined by their hydrophobicity and ionization. The sensitivity, precision, accuracy, and per-run acetonitrile consumption of the MLC method were comparable to those of the conventional HPLC method. However, the latter method exhibited higher performance for application to EL and EH samples, particularly those with low analyte concentrations and varying sample matrices. Overall, the analysis of canthin-6-one alkaloids using MLC was limited to trace analytes due to interference by the matrix.
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