As the new fluorescent stains such as SyproRuby (TM) and DeepPurple (TM) are getting widespread recognition for proteome analyses by the traditional 2-D gel method, it becomes important to test the feasibility of these stains with respect to staining reproducibility, protein quantitation, and compatibility of the stain with downstream MS. The binding of epicocconone, active ingredient of DeepPurple (TM), to one of the primary cleavage sites of trypsin (lysine residue) raises the possibility of incomplete cleavage and interference with PMF However, the current study tests and concludes that the DeepPurple (TM) stain can result in increased peptide recovery compared to SyproRuby (TM) stain and can improve MS-based identification of lower intensity proteins spots.