We previously reported that sequence and partial linkage information, including chain and blood-group types, of reducing oligosaccharides can be obtained from negative-ion electrospray CID MS/MS on a quadrupole-orthogonal time-of-flight instrument with high sensitivity and without derivatization (Chai, W.; Piskarev, V.; Lawson, A. M. Anal. Chem. 2001, 73, 651-657). In contrast to oligonucleotides and peptides, oligosaccharides can form branched structures that result in a greater degree of structural complexity. In the present work we apply negative-ion electrospray CID MS/MS to core-branching pattern analysis using nine 3,6-branched and variously fucosylated oligosaccharides based on hexasaccharide backbones LNH/LNnH as examples. The important features of the method are the combined use of CID MS/MS of singly and doubly charged molecular ions of underivatized oligosaccharides to deduce the branching pattern and to assign the structural details of each of the 3-and 6-branches. These spectra give complimentary structural information. In the spectra of [M Ϫ H] Ϫ , fragment ions from the 6-linked branch are dominant and those from the 3-linked branch are absent, while fragment ions from both branches occur in the spectra of [M Ϫ 2H]
2Ϫ. This allows the distinction of fragment ions derived from either the 3-or 6-branches. In addition, a unique D 2-3 ion, arising from double D-type cleavage at the 3-linked glycosidic bond of the branched Gal core residue, provides direct evidence of the branching pattern with sequence and partial linkage information being derived from C-and A-type fragmentations, respectively. (J Am Soc Mass Spectrom 2002, 13, 670 -679) © 2002 American Society for Mass Spectrometry T he potential role of carbohydrates in cellular events has long been hypothesized although evidence for this has only strongly emerged over the last two decades. Awareness of the biological function of oligosaccharide chains in glycoproteins, glycolipids, and proteoglycans has intensified as an increasing number of examples have been reported which reveal that carbohydrate structures participate in various biological events as well as modifying protein functions. One of the early indications of carbohydrates in recognition was binding of the influenza virus to red blood cells via sialic acid [1], and later by work on the chemical basis of the antigenicity of polysaccharides and of the well-known ABO (H) bloodgroup system [2,3] in which specificity is determined by oligosaccharides. Carbohydrates are well placed to act in cellular recognition as many cells are surrounded by an oligosaccharide layer from cell associated glyco-