The long range goal of this proposed effort is to understand the structure-functional factors related to molecular glycosylation. The specific aims are directed at analytical problems in two critical areas: methods that will enhance sample capture and detection from biological extracts, and strategies that advance analyte characterization with improved ion trapping (MSn) instrumentation. To consider the most frustrating problem in glycoprotein function, e.g., pleiotrophism, we discuss an innovative genetic approach that begins by building a proteome-glycome data base with the simple animal model, Caenorhabditis elegans. This latter effort is supported by two user groups that will provide glycosyltransferase gene mutants and knockouts to correlate visual and chemical phenotypes, and an 'in-house' geneticist for consultation. To insure an effective focus within the framework of these developments, we additionally summarize continuing applications with two user groups; infectious diseases and glycoconjugate antigen presentation. These "Focus Groups" bring the breath of analytical challenges from isolation and purification to structural characterization. The group activities represent no direct fiscal burden to this application and allow us to contribute to very important issues in immunology. Thus, the "Specific Aims" of the proposal are organized under the heading "Chemical Modifications," (for enhanced isolation and detection), and "Extending Instrumental Capabilities," (by modifications to an ion trap mass spectrometer). A third aim to understand function proposes a combined genetic and structural approach, "Defining Function in Glycobiology," by building a proteome-glycome data base using the first animal model with a defined gene sequence and fully understood cell lineage. The staff supporting for these activities bring considerable experience in each of their representative disciplines discussed in this application; instrumentation, carbohydrate chemistry, proteomics, and glycomics. Additionally, for direct consultation and backup support the University of New Hampshire has an excellent electronics and machine shop in an adjacent building, supported by NASA, a C. elegans geneticist, (Dr. John Collins), who provides worm cultures, incubator time, and genetic understanding, and importantly, a group of chemistry graduate students who seem to possess an appetite for instrumentation and biology whose training is supported by the Department.