Thyme is used worldwide both as a spice and crude drug. In addition, nowadays in the food industry it has increasing significance as a natural antioxidant. Volatile aromatic compounds of thyme have been thoroughly characterized; however, the non-volatile compounds may also contribute to the organoleptic quality and antioxidant properties. The aim of this work is to determine the phenolic acids and to profile the flavonoid compounds in the aqueous extract of two chemotypes of Thymus vulgaris L. Experiments were carried out using high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS). Predefined phenolic acids were quantified in untreated and alkaline hydrolyzed aqueous extracts. Flavonoid derivatives were qualitatively analyzed by a non-targeted screening method. Our results showed that among the phenolic acids rosmarinic acid was the main component (882-1677 μg g−1 fresh weight) and in the thymol-type samples the amount of syringic acid and rosmarinic acid was predominantly higher compared with the non-thymol type sample. Apigenin and luteolin were the major flavonoids in the extracts, which were present in the form of hexopyranuronic acid conjugates.
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