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In capillary electrophoresis (CE), a capillary is usually filled with an appropriate buffer. A sample solution is injected from the inlet end of the capillary, electric field is applied to the capillary ends, and components migrate to the detector point with different velocities due to distinctions in their electrophoretic properties. Consequently, they reach the detector at different times. Results are displayed as a sequence of peaks, where, ideally, each peak represents one compound. Peak area or peak height indicate the initial concentration of the compound in the studied mixture.

The main parameter defining differences in electrophoretic mobility of the compounds in CE is their charge-to-mass (e/m) ratio. Since this ratio is a highly specific property of compounds, CE allows a very high resolution separation and can be used to analyse almost all classes of compounds. The presence of ionizable groups (– Si – OH) on the inner surface of the fused silica capillary gives rise to a phenomenon called electroosmotic flow, which is just a bulk flow of the whole liquid inside the capillary occurring when the voltage is applied. Electroosmotic flow enables simultaneous determination of positively and negatively charged compounds in one run. Neutral compounds can also be analysed along with charged species provided that a surfactant (e.g. sodium dodecyl sulphate) is added to the buffer to form a micellar phase that facilitates their separation. This mode of CE, called micellar electrokinetic chromatography, is a very successful combination of electrophoretic and chromatographic techniques where compounds are separated based on the differences in their charge-to-mass ratio and hydrophobic/hydrophilic properties. Several other modes of CE can be performed on CAPEL instruments depending on the nature of separated solutes and general goals of the analysis. Among them are capillary gel electrophoresis, capillary isoelectric focusing, and capillary electrochromatography.

In most cases an UV lamp is used as the light source at the detector point. A monochromator gives the highest flexibility to the user enabling selection of the most appropriate wavelength for the detection and spectral scanning of the separated solutes. Compounds that do not absorb in the UV light (e.g. inorganic ions) can be analysed in the indirect mode with a certain UV – absorbing additive in the buffer.

Сapillary electrophoresis (CE) method has been generally recognized worldwide and is recommended for routine use by such organisations as British, American, and European Pharmacopoeia, World Health Organization (WHO), and the International Organisation of Vine and Wine (OIV).