A challenging aspect of structural elucidation of carbohydrates is gaining unambiguous information for anomers, linkage, and position isomers. Such isomers with identical mass can't be easily distinguished in mass spectrometry and a separation step is required prior to mass spectrometry identification. In our laboratory, gas-phase separation and differentiation of anomers, linkage, and position isomers of disaccharides was achieved using High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS). The FAIMS method responds to changes in ion mobility at high field rather than absolute values of ion mobility, and was shown to provide efficient separation and identification of disaccharide isomers at high sensitivity. Separation of analyzed disaccharide isomers can be accomplished at low nM level in a matter of seconds without sample purification or fractionation. Capability for examining a large population of ionic species of disaccharides by this method allowed for correlating structural details of disaccharide isomers with their separation properties in FAIMS. Results for disaccharide isomers indicate that this method could be applied to a larger group of carbohydrates. ( Mass spectrometry has shown a unique ability to resolve certain structural ambiguities. Permethylation is a well developed but time-consuming GC-MS method in linkage analysis of oligosaccharides [1,2]. Other methods implementing the derivatization of saccharides have been used to obtain their structural information [3][4][5][6][7][8][9][10][11]. The soft mass spectrometry ionization techniques such as fast atom bombardment (FAB) [12][13][14][15][16], liquid secondary ionization mass spectrometry (LSIMS) [17,18], along with matrix-assisted laser desorption ionization (MALDI) [19 -23], and electrospray ionization (ESI) [24 -28] have gained attention as approaches to investigate underivatized oligosaccharides. Collision-induced dissociation (CID) offers the possibility to assign details of carbohydrate structure such as sugar sequence for linear oligosaccharides [12], linkage position [12,[15][16][17]29], and differentiation of anomers [25,30]. In addition to analyzing protonated or deprotonated molecular ions of saccharides in CID, alkali metal adduct ions have been used to promote fragmentation of ligand-carbohydrate complexes. In the positive ion mode, calcium and magnesium adducts of oligosaccharides were investigated for the elucidation of the linkage position of trisaccharides [26] and cobalt complexes have been used to differentiate the anomeric configuration of disaccharides [30]. In the negative ion mode, decomposition of chloride adducts was investigated for differentiation of the linkage position of disaccharides [31].Despite recent advances in tandem mass spectrometry of carbohydrates, the spectral differences for some isomers are very small and they do not provide unambiguous identification. This is especially true when a mixture of isomers with the same m/z has to be analyzed. In such applications a separation step is required ...