The 20S core particle (CP) is composed of 28 subunits arranged in four stacked heptameric rings (alpha 7 beta 7 beta 7 alpha 7) forming a symmetrical barrel-shaped structure. Typically, in previous reports, the purification of CP mainly relied on the antibody, liquid chromatography and affinity tag-based strategies. In this study, we report a relatively simple and economical protocol for proteomic analyses of CP, which combines differential centrifugations with native-PAGE. Furthermore, it is compatible with both scaled-up purification from erythrocytes and scaled-down purification from low to around 3.0 x 10(7) pancreatic cancer cells, SW1990. In addition, a direct three-dimensional gel electrophoresis approach that omits the interval procedure between native-PAGE and IEF/SDS-PAGE is introduced. The results obtained in this study show that this protocol has a valuable potential for the studies of CP and other protein complexes.