The long-term survival of patients with chronic diseases, in particular cancer, is influenced significantly by the detection of early-stage disease. Determination of accurate protein biomarkers in biological fluids and cellular structures is of great value in early diagnosis of a disease, surveillance and asymptomatic screening, and the most promising approach to improve prognosis. Biomarker-based companion diagnostics are also becoming of great value in predicting response to treatment. Companion biomarkers are designed to identify responsive patient sub-populations or those likely to experience adverse drug effects. Using companion biomarkers yields safer and more efficacious drug products, reduces clinical trials and development costs, improves post-marketing safety profiles and salvages therapies that otherwise would not be granted approval. The advent of personalized medicine will require change in the traditional paradigms for developing and commercializing new pharmaceutical products. Today, less than 1% of current drugs have a companion diagnostic, and 60% of the drugs in clinical trials have a companion diagnostic in mind. Some drugs which have been withdrawn from market or Phase 3 development due to serious adverse events may have had a different fate if combined with a companion diagnostic to identify responders or to closely monitor toxicity. The proteome represents all the possible gene products of a cell. Any protein may exist in multiple forms that vary within a particular cell or in different cells, because of modifications derived from co-translational, post-translational, regulatory and degradative processes that affect protein structure, localization, function and turnover. Therefore, a combination of proteomic techniques should be capable to characterize all proteins in a biological system, including complex features, like isoforms, chemical or enzymatic modifications, interactions and functional structures. Immunoaffinity capillary electrophoresis (IACE), which benefits by using the power of highly selective affinity capture agents with the high-resolving power of capillary electrophoresis (CE), has demonstrated to be a useful tool for the isolation, separation, and quantification of proteins and peptides. When coupled to one or more sensitive detectors, such as a laser-induced fluorescence detector (LIF) and/or a mass spectrometer (MS), IACE is becoming an important tool for the characterization of proteins and peptides present at a wide range of concentrations in simple and complex matrices. Furthermore, when IACE-LIF and/or IACE-MS are coupled with artificial intelligence based pattern recognition systems, it could result in a powerful tool to study early changes in the underlying pathophysiology of many diseases and toxic conditions. In this seminar I will discuss the use of a multi-dimensional, multi-task immuno-separation instrument adapted to be coupled to one or more detectors, including a mass spectrometer, for the capture, separation, quantification, and characterization of protein and peptides biomarkers in biological fluids, cell extracts and exhaled breath. Furthermore, I will address the use of IACE for the analysis of isoforms, modified proteins and peptides, degradants, and protein-drug conjugates. The IACE instrument can be manufactured as a portable miniaturized point-of-care instrument to be used in doctor’s office, ambulances, and remote locations.