One promising method to prepare protein-selective polymers is the epitope-imprinting approach, where surface-accessible peptides from a target protein are used as templates to create surface-exposed binding sites on molecularly imprinted polymers (MIPs). However, selection of a suitable peptide target is not always straightforward, and synthesis of peptide on a large scale can be costly. In this work, we developed a new approach that can be used to select peptide epitopes on protein surface to be used as templates to prepare protein-selective MIPs. In this case study, human hemoglobin (Hb) was immobilized on silica nanoparticles and then fragmented by tryptic digestion. The particle-supported peptides were then used as templates to synthesize the Hb-selective MIPs, which were obtained after removal of the silica support and the peptides. The MIPs were tested in equilibrium binding experiments to evaluate their protein separation performance. The new surface imprinted MIPs displayed high selectivity for Hb, and was able to separate different variants of Hb from protein mixtures and crude cell extracts.