Mass spectrometry of glycopeptides is an efficient strategy for profiling glycans at specific sites in glycoproteins. To assess the reliability of this method for determining the fucosylation levels of glycoproteins, we conducted mass spectrometry of fucosylated glycopeptides from transferrin and haptoglobin. The biantennary glycans containing antenna alpha1,3/4 fucose or alpha1,6 core fucose showed different fragmentation behaviors in collision-induced dissociation of protonated glycopeptides. Stability was dependent on peptide backbone sequences. The major dissociation, cleavage of the GlcNAcbeta1-->2Man linkage of antenna, was evident at a slightly lower activation energy for the core fucosylated species, while the linkage of alpha1,6 core fucose was more stable than that of antenna alpha1,3/4 fucose. However, these fragmentations were induced only with sufficient loading of activation energy. The quantitation of fucosylated glycans by mass spectrometry of glycopeptides, without collisional activation, was thus justified. The fucosylation levels calculated from the signal intensities in electrospray (nanospray) ionization and ultraviolet matrix-assisted laser desorption/ionization mass spectra were essentially the same. The mass spectrometric profiling of glycopeptides from transferrin of congenital disorders of glycosylation (CDG-Ia and CDG-IIc) patients demonstrated that the elevation or reduction of fucosylation in pathological conditions can be reliably determined by MS of glycopeptides.