Capillary electrophoresis-mass spectrometry and its application to proteomic analysis

Abstract

Proteomic analysis plays an important role in basic biological studies and precision medicine. However, real samples contain numerous proteins with a wide dynamic distribution range. Such high complexity of the samples has a drastic effect on the identification coverage of proteins. Consequently, with advancements in mass spectrometry (MS) technology, concomitant improvements in separation technologies for simplifying the sample should be critical. With the advantages of small sample loading volume, high separation efficiency, and high speed, capillary electrophoresis (CE) coupled to MS has been gained much attention in the field of proteomics research. A nanoflow sheath liquid interface and a sheathless interface have been developed and commercialized, boosting the development of the CE-MS technology. Capillary zone electrophoresis (CZE), capillary isoelectric focusing (CIEF), and capillary electrochromatography (CEC) have been successfully combined with MS, and CZE-MS has widespread application. In proteomic research, the "bottom-up" strategy, which is based on the separation and identification of enzymatic peptides, is widely applied. With the limit of detection as low as 1 zmol for peptides, CE-MS has been successfully applied to single-cell proteomic analysis. Besides, CE is complementary to reversed-phase liquid chromatography (RPLC), providing a new approach for the separation and identification of peptides with similar hydrophobic properties (especially, post-translational peptides). The "top-down" strategy, which is based on the separation and identification of intact proteins, can directly provide more accurate and complete information about proteins. For protein separation, CE is advantageous in terms of the high separation resolution and high protein recovery, thereby improving the sensitivity and coverage of protein identification. Native MS enables successful identification and characterization of protein complexes under nondenaturing conditions. Because of the good compatibility of CE with MS, attempts have been made to use CE coupled with native MS for the separation and identification of protein complexes. In this review, the development of the CE-MS technology is first reported, including a robust and sensitive CE-MS interface, and a separation mode coupled to MS. Then, the application of the CE-MS technology to "bottom-up", "top-down" and native MS analysis is discussed. The superiority of CE-MS in proteomic analysis is also emphasized. Finally, the promising future prospects of CE-MS are discussed.