Peptide electrophoretic mobilities were measured at different acidic pH in water-2,2,2-trifluoroethanol mixtures. Fit of experimental mobilities according to binding equations allowed the calculation of peptide C-terminus dissociation constants and the Stokes radius of the differently protonated forms. Analysis of the data showed that the use of hydro-organic solvents in capillary electrophoresis offers the following principal advantages: (a) a modification of dissociation constants and Stokes radii that are strongly dependent upon peptide sequence and that can be conveniently utilised for selectivity manipulation; (b) an increase of separation performance arising from the stabilisation of particular peptide conformations; (c) a solubility of large apolar peptides with respect to aqueous solutions