Cellular responses originate in the nucleus where gene expression is initiated. The genetic material and its expression are managed and maintained by the nuclear proteome. We postulated that expression proteomic technologies, applied to nuclear protein extracts, would enrich our understanding of the molecular reprogramming that occurs during in vitro differentiation of human embryonic stem cells. However, this approach is challenged with the over-representation of histones and the presence of nucleic acids, both of which significantly interfere with isoelectric focusing. We have developed an effective and reproducible technique to deplete nuclear protein extracts of histones and nucleic acids in a single step. This method significantly improves the efficacy and the resolution of 2-DIGE separation, enhancing the quality of image analysis for nuclear protein extracts.