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Metabolic profiling of body fluids from small animal models is often used in (translational) biological studies in order to obtain insight into the underlying molecular mechanisms of (complex) diseases. From an analytical point of view, the profiling of (endogenous) metabolites in rat brain microdialysates is challenging because of the limited sample volume for both sample preparation and injection, notably in longitudinal studies. This service provides a CE-MS method allowing the reliable quantification of endogenous metabolites in rat brain microdialysate using direct sample injection.