The study presents the mass spectrometry application of carbon nanomaterials in proteomic research. We utilized two spherical carbon nanomaterials, C60 buckyball and iron-cored carbonball (Fe-C), in peptide sequence identification of a serum protein using matrix-assisted laser desorption ionization-time of flight mass spectrometer (MALDI-TOF-MS). The biological samples used in the experiments were enzymatically trypsinized bovine serum albumins (BSA) peptides instead of synthesized small peptide fragments. Experimental results were compared and noticeable improvements in mass spectrometry spectrum were obtained and quantified. In addition, we also utilized EDS and TEM to determine the chemical composition and morphology of nanostructure of iron-cored carbonball.