Many recent papers and reviews have confirmed the powerful coupling between CE and MS due to efficient and selective separation in combination with selective detection allowing detailed characterization of many biomolecules. It is known that CE-MS is an increasingly used and sought after technique for analysis in different fields such as environmental science, food analysis, biotechnology, pharmaceutical analysis, biomedical science, forensic science, toxicology, and genetic analysis. CE-MS is particularly used in bio-omic applications (proteomic, metabolomic, and also genomic applications) for the determination of biomarkers, disease diagnosis, and therapeutic treatment monitoring. Biomarker qualification, clinical proteomics, and its implementation in routine clinical analysis have certain limitations associated with reproducibility and analytical robustness. However, CE-MS has been successfully used in numerous clinical applications in recent years when compared with other platforms. The main advantage lies in the availability of large comparable datasets that were all obtained by using the same procedure for sample preparation, analysis, and subsequent data evaluation. The scope of this review is to discuss the performance of CE-MS as a platform for bio-omics analysis and target-based applications focusing on quadrupole (Q), IT, and TOF analyzers, and the types of bioapplications that apply to the particular analyzers. Papers and reviews that were published in 2012 and 2013 with relevant CE-MS applications are considered in this review.