This article describes the use of capillary electrophoresis (CE) to examine the influence of different cations (C+; C+ = Na+ and tetra-n-alkylammonium, NR4+, where R = Me, Et, Pr, and Bu) on the rates of denaturation' of bovine carbonic anhydrase II (BCA) in the presence of anionic surfactant dodecylsulfate (DS-). An analysis of the denaturation of BCA in solutions of Na+DS and NR4+DS- (in Tris-Gly buffer) indicated that the rates of formation of complexes of denatured BCA with DS- (BCA(D)-DSn,sat-) are indistinguishable and independent of the cation below the critical micellar concentration (cmc) and independent of the total concentration of DS- above the cmc. At concentrations of C+DS- above the cmc BCA denattifecl, at rates that depended on the cation; the rates decreased by a factor >10(4) in the order of Na+ approximate to NMe4+ > NEt4+ > NPr4+ > NBu4+, which is the same order as the values of the cmc (which decrease from 4.0 mM for Na+DS- to 0.9, mM for NBu4+ DS- in.Tris-Gly.buffer). The relationship between the cmc values and the rates of formation of BCA(D)-DSn,sat- suggesied,thatilie kinetics Of denaturation of BCA involve the association of this protein with monomeric DS- rather than with micelles of (C+ DS-)n. A less-detailed survey of seven other proteins (alpha-lactalbumin, beta-lactoglobulin A, beta-lactoglobulin B, carboxypeptidase.B; creatine phosphokinase, myoglobin, and ubiquitin) showed that the difference between Na+DS- and NR4+DS- observed vvittiBCA was'not general. Instead, the influence of NR4+ on the association of DS- with these proteins depended on the protein. The selection of the cation contributed to the properties (including the composition, electrophoretic mobility, and partitioning behavior in aqueous two-phase systems) of aggregates of denatured protein and DS-. These results suggest that the variation in the behavior of NR4+DS- with changes in R may be exploited in methods used to analyze and separate mixtures of proteins.