Imaged capillary isoelectric focusing (iCIEF) is a powerful separation technique applied frequently for the analysis of biotherapeutics. However, direct mass spectrometric characterization is usually not possible. Here, focused peaks from an iCIEF system are transferred to a four-port nanoliter valve where peaks of interest are cut and transferred directly (flow injection) or via capillary zone electrophoresis to electrospray mass spectrometry. At first, flow injection coupling was tested with a mixture of peptides showing intraday precision (RSD) of 20.0 and 3.4% in area and 15.2 and 6.3% in intensity for angiotensin I and leucine-enkephalin, respectively. For the analysis of charge variants in an intact mAb, flow injection and CZE as second dimension were compared, demonstrating the usability of flow injection even for large proteins. However, improved spectra quality was achieved when CZE-MS was applied. In this way, accurate masses were obtained not only for the main isoform, but also for the main acidic and basic variants. These results demonstrate the power of iCIEF-CZE-MS for the analysis of biotherapeutics.