Recently, nanofiltration techniques have been introduced by pharmaceutical industries in the downstream processes for peptides, to perform concentration, purification and salt/solvent exchange, and have been demonstrated as being suitable for integration with conventional chromatographic purification techniques, providing savings in terms of time and costs. Design of Experiments (DoE) methods have been extensively applied in the process design of the conventional techniques, under the so-called Quality by Design (QbD) concept, but applications of DoE methods to nanofiltration are still few. In this study, the nanofiltration of a model peptide, conventionally named PEP1, in trifluoroacetic acid/acetonitrile/water mixtures is studied by DoE. Statistical models for solvent flux, peptide and trifluoroacetic acid rejections are obtained by statistical Analysis of Variance and the best operating conditions for concentration are found by numerical optimization of the statistical models. The statistical models from DOE are included in the mathematical framework of the diafiltration process, to calculate the evolution of peptide, counter-ion and solvent concentrations over time, compare constant volume vs. variable volume diafiltration modes, and select the best process in terms of operating time and solvent consumption. This work demonstrates that empirical DoE models can provide phenomenological understanding of the transport mechanism through nanofiltration membranes for a specific solute of interest and successfully support the process modelling for concentration and diafiltration, providing a methodology to select the most appropriate filtration technique for a given separation problem. (C) 2013 Elsevier Ltd. All rights reserved.