Urea is commonly used to lyse cultured cells and solubilize proteins from a biological source. In this study, after extracting biomolecules using a lysis buffer that included urea for an effective cleaning of protein from a urea-rich protein sample, a five-flow microfluidic desalting system was applied using the metal ions of Mn2+, Zn2+ and Fe3+, which have urea affinity-capturing properties. This device effectively removed urea from the sample phase of the microfluidic channel via the diffusion, with a difference of the concentration from the sample flow to both sides of the buffer flow. and an affinity of metal ions into the urea between the buffer phase and the affinity phase. The removal efficiency for the urea was 67, 64, and 63%, with concentrations of 50 mM Mn2+, 10 mM Zn2+, and 5 mM Fe3+ metal ions in the affinity phase, respectively. In addition, protein after desalting with the microfluidic device was improved to more than 10% of the relative activity, with a significant improvement of the signal of mass spectrum shown by MALDI-MS. (c) 2006 Elsevier Ltd. All rights reserved.