Currently, feature annotation remains one of the main challenges in untargeted metabolomics. In this context, the information provided by high‐resolution mass spectrometry (HRMS) in addition to accurate mass can improve the quality of metabolite annotation, and MS/MS fragmentation patterns are widely used. Accurate mass and a separation index, such as retention time or effective mobility (μeff), in chromatographic and electrophoretic approaches, respectively, must be used for unequivocal metabolite identification. The possibility of measuring collision cross‐section (CCS) values by using ion mobility (IM) is becoming increasingly popular in metabolomic studies thanks to the new generation of IM mass spectrometers. Based on their similar separation mechanisms involving electric field and the size of the compounds, the complementarity of DTCCSN2 and μeff needs to be evaluated. In this study, a comparison of DTCCSN2 and μeff was achieved in the context of feature identification ability in untargeted metabolomics by capillary zone electrophoresis (CZE) coupled with HRMS. This study confirms the high correlation of DTCCSN2 with the mass of the studied metabolites as well as the orthogonality between accurate mass and μeff, making this combination particularly interesting for the identification of several endogenous metabolites. The use of IM‐MS remains of great interest for facilitating the annotation of neutral metabolites present in the electroosmotic flow (EOF) that are poorly or not separated by CZE.