Here we describe a technique to obtain all the N-linked oligosaccharide structures from a single reversed-phase (RP) HPLC run using on-line tandem MS in both positive and negative ion modes with polarity switching. Oligosaccharides labeled with 2-aminobenzamide (2AB) were used because they generated good ionization efficiency in both ion polarities. In the positive ion mode, protonated oligosaccharide ions lose sugar residues sequentially from the nonreducing end with each round of MS fragmentation, revealing the oligosaccharide sequence from greatly simplified tandem MS spectra. In the negative ion mode, diagnostic ions, including those from cross-ring cleavages, are readily observed in the MS 2 spectra of deprotonated oligosaccharide ions, providing detailed structural information, such as branch composition and linkage positions. Both positive and negative ion modes can be programmed into the same LC/MS experiment through polarity switching of the MS instrument. The gas-phase oligosaccharide nonreducing end (GONE) sequencing data, in combination with the diagnostic ions generated in negative ion tandem MS, allow both sequence and structural information to be obtained for all eluting species during a single RP-HPLC chromatographic run. This technique generates oligosaccharide analyses at high speed and sensitivity, and reveals structural features that can be difficult to obtain by traditional methods. . Proper structural determination is thus critical to the understanding of the biological role of carbohydrates. Although there are fewer monosaccharide building blocks in N-linked glycans than there are amino acid moieties in proteins, the combination of multiple branchings and linkages add greater complexity to the glycan structures. Such structural diversity also adds to the difficulty of structural characterization.Many analytical tools are now available for oligosaccharide characterization, such as high field NMR, liquid chromatography, capillary electrophoresis, and mass spectrometry. Although unambiguous oligosaccharide structural assignments can be made by NMR [2][3][4][5], this technique often requires large quantities of highly purified material. Typically, more than 50 mg of glycoprotein and extensive preparative fractionation are required to resolve oligosaccharide structures of relatively low abundance. A more common characterization approach utilizes sets of specific exoglycosidases, which cleave terminal monosaccharides from the nonreducing end, followed by chromatographic or MS analysis [6][7][8]. In this approach, the sequence of the oligosaccharide chain is revealed, either through sequential removal of monosaccharides from the chain upon successive enzyme treatment, or from the oligosaccharide ladder generated upon treatment with an array of enzymes. Linkage positional information and anomericity of the terminal monosaccharide can also be obtained, based on the specificity of the exoglycosidases used. Unfortunately, this classic sequencing technique is often labor intensive, time consuming, and...