This review focuses on rapid, efficient, and sensitive characterization of the proteome by capillary electrophoresis (CE) and microchip capillary electrophoresis (MCE) in conjunction with laser-induced fluorescence (LIF). A number of advanced CE-LIF and MCE-LIF techniques, including on-column concentration techniques, on-line chemical reaction and enzyme-assay techniques, integrated microdevices, and high-efficiency multidimensional separation techniques that have been developed within the past few years, are capable for the analysis of trace proteins in biological samples and/or in single cells. These powerful techniques also show great potential for drug screening and diagnosis. The basic principle of each technique and its advantages and shortcomings for proteomics studies are discussed in detail. We also highlight the importance of techniques that possess improved analytical sensitivity, sample throughput, and quantitation capabilities for identifying the complexities and dynamics of the proteome expressed by cells, tissues, or an organism.