Objective: With considering about our extended information in genome sequence field which gathered in genome data banks nowadays discovering the genes function and their products still unclear that’s why study in this area sensed. Proteomics researches are one of the powerful tools for reach to this knowledge Materials and Methods: In our study at first we prepare competent cells from Escherichia coli species named BL21 for expressing recombinant protein, then in several stages, essential condition for processing recombinant protein, of this sort; change in culture temperature, induction time and concentration of IPTG for protein expression, time and number of sonication pulses for breaks in bacterial membrane and releasing cytosolic contents ,at least change in kind and concentration of detergents for eliminate membrane debris were adjusted. All of the results step by step classified and optimized. Results: The optimized concentration of IPTG was 0.1 mM. There was not any significant difference between the used detergents as both of them had the same effect on permeabilization of the bacterial membranes. Finally we detected the recombinant GST-PEP by SDS page analysis with both of Commasie Brilliant Blue staining (CBB) and western blot using anti GST antibody. Conclusion: Taken together these data showed that PEP (peroxisomal protein)which containing fibronectin type III and two hy<font>drop</font>hobic domains should be assessed by further proteomics analysis to discover it's interactions with other proteins in neural stem differentiated cells.