This study aims to assess and qualitatively compare the visual presentation of chromatographic data from the isomerisation of natural pyrethrins – a group of pesticides derived from Chrysanthemum flowers – using one-dimensional gas chromatography (1DGC) and comprehensive two-dimensional gas chromatography (GC×GC). Molecular structural changes, such as thermal isomerisation in this case, occur during gas chromatography injection and separation, to provide characteristic patterns which may not be routinely recognised on the 1D chromatogram. To demonstrate the influence of analytical method parameters on isomerisation processes, variations in oven temperature (isothermal vs. temperature programmed analysis), inlet mode (split vs. splitless), inlet temperature, and carrier gas flow rate were investigated. Increasing oven temperature was the most significant factor affecting isomerisation. Splitless injection mode and increasing inlet temperature promoted isopyrethrin formation, while the effect of inlet temperature appeared minimal with a split injection technique, most likely due to the short residence time in the inlet. Increased carrier gas flow rates in a temperature programmed analysis reduced retention time and minimised isomerisation. The unique presentation of isopyrethrin peaks on a GC×GC contour plot allows for facile recognition of isomerisation especially at low concentrations, simplifies chromatogram interpretation, and aids in analyte identification. It also confirms that the isomerisation process is irreversible since the pyrethrin I and II compounds are absent throughout the bridge formation. These benefits support the use of GC×GC over 1DGC to study isomerisation. Additionally, due to limited data in the literature, Kováts retention indices and linear retention indices of the natural pyrethrins, including isopyrethrins, were experimentally determined on four columns: DB-5 ms UI, Rxi-17Sil MS, SLB-IL60i, and SLB-IL111i.
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