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The structural diversity of lipids presents significant challenges for accurate identification and characterization, ne-cessitating advanced analytical tools. Among these challenges is the differentiation between cis and trans isomers of lipids, which differ only by the geometry of a carbon-carbon double bond. This study employs ozonolysis kinetics to distinguish these isomers based on the reactivity of their gas phase ions with ozone. To achieve precise differentia-tion, it is essential to use an ion adduct that enhances reactivity, thereby improving the sensitivity of the kinetic assays. We evaluated various ion types, including protonated lipids as well as lipids cationized with lithium, sodium, and potassium, using a modified quadrupole ion trap mass spectrometer. Our results demonstrate that lithium-adducted lipids exhibit the highest reaction efficiency and greatest sensitivity for distinguishing between cis and trans isomers. Subsequent analysis of cis and trans isomer mixtures of PC 18:1/18:1 (Δ9), PC 16:1/16:1 (Δ9), and PC 14:1/14:1 (Δ9) confirmed the method's robustness.