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A novel strategy, based on the use of isobaric labeling, is introduced for quantitative glycomics. In this approach, glycans are permethylated with either 13CH3I or 12CH2DI. This pair of reagents has the same nominal mass but differ in their exact mass by 0.002922 Da per label. This mass difference is difficult to resolve with current mass spectrometers in cases where only a single label is attached to the analyte. However, glycans typically contain multiple hydroxyl groups, which increase the mass difference between the two samples. Since the number of hydroxyl groups increases with the mass of the glycan, the difference between these isobaric species also increases and thus the resolution needed is approximately 25,000 ΔM/M and is independent of the glycan’s size for typical N- and O-linked species. The advantages of this labeling strategy are numerous, and result primarily from the isobaric ions appearing at the same nominal mass-to-charge ratio. This characteristic leads to increased ion intensity as ions from both samples are not distributed between isotopic species having different m/z values. The small mass difference between these isobars allows the two species to be simultaneously selected for MSn analysis, permitting the relative quantitation of isomeric glycans. This procedure was successfully used to analyze N- and O-linked oligosaccharides released from a standard glycoprotein and from human serum. This strategy is directly applicable to oligosaccharides from other sources, such as glycolipds. The concept of isobaric labeling is expected to be applicable to other types of “omics” analyses with other derivatizing agents.