Electrospray ionization (ES) with a quadrupole ion trap (qIT) mass analyzer has been considered to be an improved instrumental approach to understand the details of carbohydrate structure. To evaluate this feature, multiple samples were prepared at the BUSM Resource and brought to laboratories that were successfully using a LCQ (Finnigan) Paul ion trap. Samples, including GSL, N-, and 0-linked glycans were extracted or released from glycoproteins, andmethylated. Extensive effort was focused on internal core branching of complex glycans to ascertain linkage detail. Two papers describing this work have been accepted for, publication. In onereport, an isomeric disialyl glycosphingolipid samples was evaluated for s6quence, branching andlinkage information. Results were obtained that were qualitatively comparable with triple quadrupole instruments (Qlq2Q3) with major carbohydrate fragments from CI-O glycosidic rupture and additional fragments that provided a determination of sphingosine and N-acyl heterogeneity of the ceramide moiety. In unique contrast, however, the qIT extended carbohydrate understanding through MS' studies providing for the first time pyran cross-ring cleavages that define inter-residue linkage structure for glycolipids. This was achieved by selecting secondary fragments (MS3), free from the energy sinks of facile bond rupture that dominate product ion spectra. Isolation and activation of these substructures result in a more uniform distribution of fragments, providing structural insights previously inaccessible by tandem mass spectrometry. In studies with complex and branched glycans, the feature of MS' exposed structural features not available with tandem instrumentation, and from the glycoprotein fetuin, clarified an existing controversy in triantennary branching topology. This technology appears to provide a significant step toward the goal of understanding aH aspects of carbohydrate structure in a single instrument.
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