In response to physical or chemical stimuli, physiological functions can be modified by short- or long-term regulation. The former requires the activation of proteins by post-translational modification and the latter requires the induction of newly synthesized proteins. Therefore, functional proteomic studies are suitable for exploring the proteins or peptides involved in long-term regulations but are not for those involved in short-term regulations. Even though functional proteomics can be used in studying the proteins involved in long-term regulations, detection of small amount of functional proteins is still limited. Therefore, conventional methods of protein concentrations may be applied to improve resolution. Current understanding of post-translational modification includes phosphorylation, glycosylation, lipidation, and nitration. In the future, the application of post-translational modification to proteomics may improve current pitfalls on separation/purification and further explores the proteins involved in short-term regulations.