Urine proteome analysis by two-dimensional gel-based protein separation coupled with nLC-ESI-MS/MS

Three steps are especially important for the comprehensive analysis of urine proteome: protein concentration from urine with minimal loss; protein separation to reduce sample complexity; and peptide sequencing with high mass accuracy and rapid scanning. In the present study, we employed a two-dimensional gel-based approach coupled with nLC-ESI-MS/MS for the analysis of the urine proteome. The "standard" urine sample collected in Mosaiques Diagnostics within the European Urine and Kidney Proteome (EuroKUP) consortium was employed to facilitate data comparison and evaluation. In the first dimension, proteins were separated using preparative polyacrylamide gel electrophoresis, into 5 mass groups: MW