Capillary zone electrophoresis (CZE) is a convenient experimental tool for mimicking the low-throughput in vitro skin model used to optimize the delivery of peptides by transdermal iontophoresis. This paper is devoted to the extraction of pertinent molecular parameters from CZE experiments at different pH values, the optimization of CZE experimental conditions, and the development of an in silico filter useful for drug design and development. The effective mobility (mu(eff)) of ten model dipeptides was measured by CZE at different pH values, enabling to determine their pK(a) values, charge and mu(eff) at any pH. The best linear correlation between the electromigration contribution to transdermal iontophoretic flux (J(EM)) measured across porcine skin with donor and acceptor compartments at pH 7.4 and charge/MW ratio was obtained at pH 6.5, which seems to be the most suitable pH to mimic the in vitro skin model. Therefore, the experimental strategy can be considerably shortened by using a single mu(eff) measurement at pH 6.5 as a predictor of J(EM). Additionally, pK(a) prediction software packages offer a fast access to charge/MW ratio using consensual molecular charges at pH 6.5, which suggests that this simple in silico filter can be used as a preliminary estimation of J(EM).