Sometimes excessive detergent interferes with membrane protein activity and stability, and has to be removed. This should be done with caution because most membrane proteins will aggregate and precipitate if the detergent is completely removed. The concentration of detergent should be kept above the critical micelle concentrations (CMCs) so that the membrane proteins are still protected by the detergent micelles.

In other instances, detergents need to be removed when membrane proteins are reconstituted into phospholipid vesicles or nanodiscs. Detergents with high CMCs are generally preferred because they are easier to remove thereby facilitating the reconstitution of the membrane proteins into lipid bilayers.

Whether detergents are easy or difficult for removal by dialysis is dependent on their CMCs. Detergents with high critical micelle concentrations (>1 mmol/L), such as cholates and octyl glucosides, can be easily removed by dialysis or ultrafiltration. Detergents with low critical micellar concentrations (<1mmol/L), such as nonionic detergents Triton X-100, C12E9 and dodecyl maltoside are difficult to be removed by dialysis and ultrafiltration. In these cases, either solid matrix material or gel filtration can be applied for detergent removal.

In some cases, a detergent needs to be replaced by another if the original one is not suitable for subsequent chromatography or analysis. For example, ionic detergents have to be replaced by non-ionic or zwitterionic detergents, as ionic detergents are incompatible with ionic exchange chromatography and isoelectric focusing. Some detergents are more favorable for crystallization or cryo-EM analysis, so detergent exchange is often a step in the purification procedure of membran protein for structural biology studies.