The micelle velocity is defined by:
where  is the electrophoretic velocity of a micelle.
The retention time of a given sample should depend on the capacity factor, :
where   is the total number of moles of solute in the micelle and  is the total moles in the aqueous phase.  The retention time of a solute should then be within the range:
Charged analytes have a more complex interaction in the capillary because they exhibit electrophoretic mobility, engage in electrostatic interactions with the micelle, and participate in hydrophobic partitioning.
The fraction of the sample in the aqueous phase, , is given by:
where  is the migration velocity of the solute.  The value  can also be expressed in terms of the capacity factor:
Using the relationship between velocity, tube length from the injection end to the detector cell (), and retention time, ,  and , a relationship between the capacity factor and retention times can be formulated:
The extra term enclosed in parentheses accounts for the partial mobility of the hydrophobic phase in MEKC.  This equation resembles an expression derived for  in conventional packed bed chromatography:
A rearrangement of the previous equation can be used to write an expression for the retention factor:
From this equation it can be seen that all analytes that partition strongly into the micellar phase (where  is essentially ∞) migrate at the same time, .  In conventional chromatography, separation of similar compounds can be improved by gradient elution. In MEKC, however, techniques must be used to extend the elution range to separate strongly retained analytes.
Elution ranges can be extended by several techniques including the use of organic modifiers, cyclodextrins, and mixed micelle systems.  Short-chain alcohols or acetonitrile can be used as organic modifiers that decrease  and  to improve the resolution of analytes that co-elute with the micellar phase.  These agents, however, may alter the level of the EOF.  Cyclodextrins are cyclic polysaccharides that form inclusion complexes that can cause competitive hydrophobic partitioning of the analyte.  Since analyte-cyclodextrin complexes are neutral, they will migrate toward the cathode at a higher velocity than that of the negatively charged micelles.  Mixed micelle systems, such as the one formed by combining SDS with the non-ionic surfactant Brij-35, can also be used to alter the selectivity of MEKC.