The study of the human metabolome requires improved analytical methods dedicated to the most polar metabolites. Due to their very low lipophilicity, and often their ionizable nature, this type of compound remains a real challenge for conventional chromatographic methods. Since charged molecules can be influenced by electric fields, electro-assisted extraction and separation methods open new perspectives for the analysis of ionizable polar metabolites. The purpose of this thesis work was to develop new metabolomic tools for the analysis of the polar ionizable fraction of the human metabolome. In a first part, we focused on the evaluation and development of new electromembrane extraction set-ups. Then we studied new approaches for the analysis of charged metabolites by capillary electrophoresis-mass spectrometry with a special focus on the challenge represented by features annotations in untargeted metabolomic analysis.