Direct chemical profiling and protein identification from living single cells using mass spectrometry (MS) have been demonstrated to further our understanding of biological variability and differential susceptibility to several diseases and treatments. Despite the great challenge from extremely complicated cytoplasm, we recently proposed a versatile MS strategy to achieve direct mass spectrometric characterization of both proteins and metabolite-like small molecules directly from living cells or single cells. Although the capability to directly handle cell cytoplasm was presumably attributed to microelectrophoresis in our previous studies, the assumption had only been partially explored by some preliminary experiments. To better understand the mechanism, herein, we systematically characterized its separation behavior with a series of model compounds covering a wide range of molecular size. With the merit of in situ separation, microelectrophoresis herein has been further demonstrated as an attractive and alternative tool, which can potentially contribute to direct MS measurements of more protein interactions or metabolic pathways in living single cells or a few cells.