The use of ultrafiltration (UF) in downstream processing becomes increasingly important. Downstream processing involves complex biological mixture which can not be well-known with simple analytical techniques. That leads to very poor theoretical data on the UF of such solutions. As a consequence, the integration of this operation in downstream processing is somewhere limited and empirical, requiring a lot of experiments. This paper proposes a new method to overcome this difficulty and to transpose data obtained in a laboratory set-up to a larger pilot unit. The approach is based on non steady state mass balance equations. On the assumption of constant transmission rates, these equations can be analytically solved. When these assumptions are not accurate, a numerical resolution is proposed. In this study, the simulated results are faced with experimental data obtained with a synthetic bio-solution constituted from a protein hydrolysate (yeast extract) and beta-lactoglobulin, filtered on an inorganic Carbosep membrane (cut-off 15 kDa). The contribution of this method to simulate and scale-up UF units is discussed.