This paper describes the applications of multifunctional magnetic nanoparticles (MNPs) for the enrichment of low-abundance proteins for polyacrylamide gel electrophoresis (PAGE) separation. The hemoglobin-functionalized MNPs, named Hb-MNPs, were obtained based on electrostatic interactions and covalent binding between the hemoglobin (Hb) and the MNPs. It was demonstrated that the proteins in human serum were selectively conjugated to Hb-MNPs, which can be used for the selective enrichment of low-abundance proteins. Three and seven kinds of proteins were identified by MS after 1-D and 2-D PAGE, respectively. Comparing with native PAGE without the treatment of MNPs, some proteins were observed, such as human serum amyloid P component (SAP), vitamin D-binding protein, and serine peptidase inhibitor. Because the high concentration of SAP can be considered as a signal for the neurodegeneration of Alzheimer's disease, the present Hb-MNPs-based method was applied to investigate the serum level of SAP for the diagnosis of Alzheimer's disease, and the results are satisfying.