It can also be used to separate various drugs based on their rate of migration through a given medium.

CE is part of a family of related techniques that use very narrow capillaries and buffers to perform high-efficiency electrophoretic separation of both small and large molecules. The separations occur through the use of high voltages, which creates electroosmotic flow (EOF) within the buffer solutions and ions inside the capillary tubing.

EOF is considered the driving force behind capillary electrophoresis, and results in the simultaneous analysis of anions, cations, and neutral charged molecules in a single analysis.

CE shares characteristics with traditional polyacrylamide gel electrophoresis (PAGE) and high-performance liquid chromatography (HPLC). In fact, CE and gel electrophoresis (GE) are considered to be in the same family. But, CE is generally seen as the faster method, providing higher throughput and resolution because the thin tubing used offer a higher surface-to-volume ratio than gels.

In contrast to the slab gels used in GE, capillary electrophoresis systems and instruments utilize these thin capillary tubes, or silica capillaries, to speed up the electrophoretic process. The tube can dissipate heat more quickly as well, allowing for higher voltages to run without any risk of overheating.

The high-voltage environment increases the velocity at which a molecule passes through the capillary, shortening the separation process and making CE highly efficient.

As well, capillary electrophoresis uses modern data acquisition devices to observe the ions as they pass through the capillary past the detector. The signal is recorded and sent to a computer with software for digital collection and analysis. The device requires very little amounts of a sample to work, so you can potentially save more money when using high-cost materials.

Furthermore, many capillary electrophoresis instruments are automated, consume limited amounts of reagents, offer precise quantitative analysis, and process a larger variety of analytes in comparison to other separation techniques. The automation is seen as advantageous to any laboratory that works with high-cost materials and is concerned with efficiency and high-resolution.

Below are the basic CE instrument components, as well as the common applications of capillary electrophoresis.