Capillary electrophoretic separations offer various modes, each with unique applications. These modes include capillary zone electrophoresis, capillary gel electrophoresis, capillary array electrophoresis, capillary isoelectric focusing, capillary isotachophoresis, micellar electrokinetic chromatography, and capillary electrochromatography.

Capillary zone electrophoresis (CZE) separates ionic components based on their electrophoretic mobility. It has been used to separate proteins, amino acids, and carbohydrates in minimum time, making it a major technique in the rapidly expanding field of proteomics. For example, it is used for protein analysis in urine samples to diagnose chronic kidney and coronary artery disease.

Capillary gel electrophoresis (CGE) is performed in a porous gel polymer matrix. It provides a molecular sieving action to separate macromolecules like proteins, DNA fragments, and oligonucleotides that have similar charges but differ in size. CGE plays a significant role in DNA sequencing, particularly in the Human Genome Project.

Capillary array electrophoresis (CAE) operates multiple capillaries in parallel for DNA sequencing. DNA is fragmented and labeled with fluorescent dyes, with the sequence determined by the dye color sequence of the eluting fragments.

Capillary isoelectric focusing (CIF) mode separates amphiprotic species, such as amino acids and proteins that contain weak carboxylic acid and weak-base amine groups. Amphiprotic compounds can donate or accept protons; in amino acids, this amphiprotic behavior results in a zwitterion with both positive and negative charges. The zwitterion does not migrate in an electric field when the solution's pH equals its isoelectric point (pI), making the pI a key characteristic in separating such molecules. Separations are based on differences in equilibrium properties of the analytes rather than migration rates.

Capillary isotachophoresis (CITP) separation mode focuses on the equal velocity migration of all analyte bands, separating either cations or anions but not both. Analyte ions migrate with unique velocities, forming adjacent bands that ultimately move at the same velocity.

The micellar electrokinetic chromatography (MEKC) technique overcomes CZE's limitation of not being able to separate neutral species by adding a surfactant like sodium dodecyl sulfate (SDS) to the buffer solution. The separation mechanism is similar to liquid chromatography (LC), depending on differences in distribution constants between the mobile aqueous phase and the hydrocarbon pseudo-stationary phase. MEKC has been used to separate a wide variety of samples, including mixtures of pharmaceutical compounds, vitamins, and explosives.

An alternative method for separating neutral compounds is capillary electrochromatography (CEC). In CEC, capillary tubes filled with silica particles ranging from 1.5 to 3 mm in size and coated with a nonpolar stationary phase are utilized. The separation of neutral species occurs as they distribute themselves between the stationary phase and the buffer solution, the latter acting as the mobile phase due to electroosmotic flow. The separation process is similar to high-performance liquid chromatography (HPLC), yet it does not require high-pressure pumps. Additionally, CEC offers superior efficiency and reduced analysis times compared to HPLC.

These various modes of capillary electrophoresis offer a versatile range of applications, from separating charged species in CZE to separating neutral species in MEKC and CEC, as well as size-based separations in CGE.