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Here, EKS is successfully paired with ESI\u2010MS\/MS to provide a sensitive and robust method for analysis of biogenic amines in biological samples. Injection parameters including electric field strength and the buffer compositions used for the separation and focusing were investigated to achieve suitable resolution, high sensitivity, and compatibility with ESI\u2010MS. Using EKS, the sensitivity of the method was improved 5000\u2010fold compared to a conventional hydrodynamic injection with CZE. The separation allowed for baseline resolution of several neurotransmitters within 16 min with LODs down to 10\u00a0pM. This method was applied to targeted analysis of seven biogenic amines from rat brain stem and whole <jats:italic>Drosophila<\/jats:italic> tissue. 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