Three systems of trace separation are used as case studies to investigate the effect of mass transfer during the blowdown step. The systems are simulated from start (clean columns) to cyclic steady state with the desorption step period equal to the adsorption step period as a base case. There is no difference between the case where mass transfer is accounted for and the case where the frozen solid condition is assumed. However, in the context of optimal operation there is a significant effect for some combinations of the desorption time period and the blowdown time period, but this effect depends on the specific system and the specification of the product purity. There is also a possible effect when the repressurization step is performed with product instead of feed.