Using molecular ion intensity from low energy electron ionisation to investigate structural isomers in Citrus

The analysis of isomers in Citrus remains challenging due to chemical diversity and structural similarity under conventional 70 eV electron ionisation (EI) conditions. This study investigated electron energies down to 5 eV and evaluated the impact of manual tune on molecular ion (M +• ) repeatability using gas chromatography-quadrupole time-of-flight mass spectrometry (GC-QTOF/MS). Thirty-one representative Citrus isomers were used to optimise EI source parameters: emission current, electron energy, and ion source temperature. Manual tune improved M +• repeatability, reducing RSD from 15.4 to 18.5% to 1.8%. The optimised low energy EI method (typically 11–12 eV, 175–195 °C) achieved favourable M +• intensities with RSD below 5.5%. Comparisons across structurally related compounds revealed that conjugation and trans -configuration enhance M +• stability, whereas allylic hydroxyl groups reduce it. This low energy EI approach improves M +• preservation and repeatability, providing a promising option for isomer differentiation in complex Citrus volatile profiles. • Effect of ion souce parameters on molecular ion intensity and its reproducibility. • The molecular ion intensities of aliphatic alcohols and aldehydes were investigated. • The molecular ion intensities of homologous aliphatic 2,4-dienals were studied. • The molecular ion intensities of monoterpene structural isomers were compared. • Low energy electron ionisation was applied to explore structural isomers in Citrus.