Abstract
We have acquired multi‐stage mass spectra (MS^n^) of four branched N‐glycans derived from human serum IgG by matrix‐assisted laser desorption/ionization quadrupole ion trap time‐of‐flight mass spectrometry (MALDI‐QIT‐TOF‐MS) in order to demonstrate high sensitivity structural analysis. [M + H]^+^ and [M + Na]^+^ ions were detected in the positive mode. The detection limit of [M + Na]^+^ in MS/MS and MS^3^ measurements for structural analysis was found to be 100 fmol, better than that for [M + H]^+^. The [M + H]^+^ ions subsequently fragmented to produce predominantly a Y series of fragments, whereas [M + Na]^+^ ions fragmented to give a complex mixture of B and Y ions together with some cross‐ring fragments. Three features of MALDI‐QIT‐CID fragmentation of [M + Na]^+^ were cleared by the analysis of MS/MS, MS^3^ and MS^4^ spectra: (1) the fragment ions resulting from the breaking of a bond are more easily generated than that from multi‐bond dissociation; (2) the trimannosyl–chitobiose core is either hardly dissociated, easily ionized or it is easy to break a bond between N‐acetylglucosamine and mannose; (3) the fragmentation by loss of only galactose from the non‐reducing terminus is not observed. We could determine the existence ratios of candidates for each fragment ion in the MS/MS spectrum of [M + Na]^+^ by considering these features. These results indicate that MS^n^ analysis of [M + Na]^+^ ions is more useful for the analysis of complicated oligosaccharide structures than MS/MS analysis of [M + H]^+^, owing to the higher sensitivity and enhanced structural information. Furthermore, two kinds of glycans, with differing branch structures, could be distinguished by comparing the relative fragment ion abundances in the MS^3^ spectrum of [M + Na]^+^. These analyses demonstrate that the MS^n^ technology incorporated in MALDI‐QIT‐TOF‐MS can facilitate the elucidation of structure of complex branched oligosaccharides. Copyright © 2005 John Wiley & Sons, Ltd.