The evaluation of the state of a biological sample before starting the complex analyses is a crucial step in proteomics studies. This paper compares planar polyacrylamide gel electrophoresis (SDS-PAGE) and capillary on-the-chip SDS GE (CGE-on-the-chip) in terms of the speed of analysis, sensitivity and flexibility. Snake venoms, which are heterogeneous with high bioactivity and consist mainly of proteins with a molecular weight mass range below 100 kDa, were investigated. CGE-on-the-chip was found to be a faster and more stable technique, providing more information than classical SDS-PAGE. CGE-on-the-chip was also capable of detecting many compounds over a broad molecular weight mass range whereas the SDS-PAGE is more time-consuming and provides acceptable resolution either in the very low (below 17 kDa) or in the mid- to high-molecular mass region (16–200 kDa) depending on the gel/buffer-system selected.