The major drawback of capillary electrophoresis (CE) for the analysis of low abundance metabolites in biological fluids is the poor concentration limits of detection (LODs). Several strategies have been developed to enhance CE sensitivity. Concerning the increase of sample volume injection, chromatographic-based preconcentration using on-line solid-phase extraction capillary electrophoresis (SPE-CE) is the best alternative to provide high concentration factors and good reproducibility for analytes with a wide range of properties. In addition, SPE-CE can be used for on-line sample clean-up and purification, with minimum sample handling. This chapter presents a workflow for untargeted SPE-CE-MS-based metabolomics, which includes sample pretreatment, SPE-CE-MS analysis, feature finding, statistical analysis and metabolite identification. In particular, the potential of SPE-CE-MS with a commercial chromatographic C18 sorbent for untargeted metabolomics is demonstrated by analysing low molecular mass compounds in plasma samples from mice genetically modified to develop Huntington's disease (HD), an inherited neurodegenerative disorder. Furthermore, the application of advanced chemometric data analysis tools, such as multivariate curve resolution alternating least squares (MCR-ALS) and partial least squares discriminant analysis (PLS-DA), is proposed for assisting the identification of metabolite biomarker candidates.