The efforts of the past funding cycle have initiated a congruent and unique strategy for sequencing oligosaccharides with all components of structure defined using an ion trap mass spectrometer (MSn). In support of this mining effort, work was initiated to build a fragment library that assimilates, and retrieves spectra in a data-confirming, bottom-up approach consistent with HTP analysis. Carbohydrate MSn data and the pathways of disassembly provide details of monomer relationships, their stereochemistry, and overall topology. In a reverse manner these pathways are trails to the precursor ion for which code has been written to define molecular structure. Such algorithms have solved selected glycan topology, de novo, on new and unusual structures in less than one second. We are at an exciting point in our research, but this effort needs strengthening with additional and generally applicable computer tools for data handling and a larger set of synthetic standards and tissue samples for library expansion. Building a library of oligomer fragments and writing more specific code is a major investment of resources and man power, but it is an essential next step toward confirmation, and fundamental as we move to sequence automation. . We continue our fundamental interest in applications, not only as a proof of principle, but to confront the demanding pleotrophic involvement in carbohydrate structures. Particularly challenging are the known spatial and temporal patterns of expression that are displayed by carbohydrate epitopes during periods of cellular development. To tackle this research area we introduce a new and more appropriate animal model Daphnia. We discuss the many reasons this simple microcrustacean is appropriate for the tasks ahead and supply preliminary data supporting this proteomic-glycomic challenge. Daphnia bridges the span between genes and molecular and cellular functions with tractable and well-characterized ecologies and displayed phenotypes. In collaboration and as members of the Daphnia Genomics Consortium (an international network of investigators committed to developing the model system) we anticipate supporting an array of gene KOs and phenotypes appropriate for developmental discovery, comparable to the role we now play with C. elegans.
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