Affinity capillary electrophoresis (ACE) refers to a number of techniques which rely on specific and nonspecific binding interactions to facilitate separation and detection through a formulary approach in accordance with the theory of electromigration. Using the intermolecular interactions between molecules occurring in free solution or mobilized onto a solid support, ACE allows for the separation and quantitation of analyte concentrations and binding and dissociation constants between molecules. As affinity probes in CAE, fluorophore-labeled compounds with affinities for the target molecules are employed. With ACE, scientists hope to develop strong binding drug candidates, understand and measure enzymatic activity, and characterize the charges on proteins. Affinity capillary electrophoresis can be divided into three distinct techniques: non-equilibrium electrophoresis of equilibrated sample mixtures, dynamic equilibrium ACE, and affinity-based ACE.
Nonequilibrium electrophoresis of equilibrated sample mixtures is generally used in the separation and study of binding interactions of large proteins and involves combining both the analyte and its receptor molecule in a premixed sample.
These receptor molecules often take the form of affinity probes consisting of fluorophore-labeled molecules that will bind to target molecules that are mixed with the sample being tested. This mixture, and its subsequent complexes, are then separated through capillary electrophoresis. Because the original mixture of analyte and receptor molecule were bound together in an equilibrium, the slow dissociation of these two bound molecules during the electrophoretic experiment will result in their separation and a subsequent shift in equilibrium towards further dissociation. The characteristic smear pattern produced by the slow release of the analyte from the complex during the experiment can be used to calculate the dissociation constant of the complex.
Dynamic equilibrium ACE involves the combination of the analyte found in the sample and its receptor molecule found in the buffered solution in the capillary tube so that binding and separation only occur in the instrument. It is assumed for dynamic equilibrium affinity capillary electrophoresis that ligand-receptor binding occurs rapidly when the analyte and buffer are mixed. Binding constants are generally derived from this technique based upon the peak migration shift of the receptor which is dependent upon the concentration of the analyte in the sample.
Affinity-based capillary electrophoresis, also known as capillary electroaffinity chromatography (CEC), involves the binding of analyte in sample to an immobilized receptor molecule on the capillary wall, microbeads, or microchannels. CEC offers the highest separation efficacy of all three ACE techniques as non-matrixed sample components are washed away and the ligand then be released and analyzed.  
Affinity capillary electrophoresis takes the advantages of capillary electrophoresis and applies them to the study of protein interactions. ACE is advantageous because it has a high separation efficiency, has a shorter analysis time, can be run at physiological pH, and involves low consumption of ligand/molecules. In addition, the composition of the protein of interest does not have to be known in order to run ACE studies. The main disadvantage, though, is that it does not give much stoichiometric information about the reaction being studied.