Ultrahigh resolution MALDI-FT-ICR profiles were obtained from human serum samples that were processed using a fully automated RPC18-based magnetic bead method. Proteins were profiled from m/z value 6630 with a resolving power of 73 000 up to m/z value 12 600 with a resolving power of 37 000. In this study, a detailed evaluation was performed of the isoforms of apolipoprotein C-III, i.e. the different mucin-type core 1 O-glycans with the addition of one or two sialic acid residues. The MALDI-FT-ICR profiles are discussed with regard to reproducibility of the signal intensities as well as the accurate mass measurements. ESI-FT-ICR-MS/MS analyses of the same serum samples were performed to confirm the identity of apolipoprotein C-III glycoforms.