A new process to produce magnetite partially coated with strawberry-like gold nanoparticles in aqueous media is reported. The fast response to magnetic fields and optical properties of gold nanoparticle-based colloidal systems are the two main advantages of this new Fe@Au nanomaterial. These advantages allow for the use of this new colloidal nanomaterial for various purposes in proteomics and biomedicine, as proteins can bind to the surface, and the surface can also be functionalized. As proof-of-concept, the new Fe@Au nanoparticles have been assessed in biomarker discovery as a tool for pre-concentration and separation of proteins from complex proteomes. To this end, sera from healthy people were compared with sera from patients diagnosed with multiple myeloma. The application of this new Fe@Au nanomaterial combined with mass spectrometry has allowed for the identification of 53 proteins, and it has also shown that the heat shock protein HSP75 and the plasma protease C1 inhibitor are potential biomarkers for diagnostics and control of multiple myeloma progression.