The advent of sugar-immobilized gold nano-particles (SGNPs), lipid-based nanoparticles, nano-chromatography and nano-electrophoresis has revolutionized the methodology for protein purification and proteomic research. This review provides an overview on the effective method developed for fast purification of protein from extracts using SGNPs. In addition, the current application of microfluidic systems for analytical purposes in biochemistry will also be explored that include the micro total analysis systems (µ-TAS) and lab-on-a-chip (LOC) analyses which are capable of isolation and detection of protein at the nanogram level. Finally, we describe why the lipid-based nano-particles (LBNPs) can enable the analysis in microchip electroseparation and how anionic and cationic LBNPs can be used for protein separation.