A standing wave design (SWD) method and an experimental shortcut design method are developed in this study for SMB systems with nonlinear isotherms and mass-transfer effects (nonideal systems). In the SWD, the mass-transfer correction terms derived in a previous study for linear, nonideal systems are incorporated into the design equations for nonlinear, nonideal systems. The SWD requires accurate isotherm and mass-transfer parameters to ensure high product purity and high yield. If these parameters are unknown, the experimental shortcut design can be applied. Frontal experiments with a binary mixture at a fixed feed concentration and three or more different flow rates are needed to formulate a series of empirical correlations for the SMB design. The two methods were tested for the binary separation of phenylalanine and tryptophan. Both rated model simulations and experimental data showed that high product purity (99.1% - 100 %) and high yield (96.3 % - 100 %) were achieved in both methods. The experimental shortcut design method is simpler than the SRD, but is limited to a fixed feed concentration. A dimensionless number is derived to quantify the deviation of an actual nonideal system from a system without mass-transfer effects (ideal system). If the dimensionless number has a value greater than 0.005 for the binary amino acid separation, the system deviates from its corresponding ideal system and the design considering mass-transfer effects gives significantly higher purity and yield than the ideal design.