Course Summary

The human genome is complete, and contains many fewer open reading frames than many expected, in part because multiple functions can derive from a single gene sequence as a result of splice isoforms, post-translational modifications, and the formation of different functional complexes with overlapping components. If we are to build-up a complete protein functional map, students must be able to: identify proteins in complexes; identify their post-translational modifications; determine the surfaces of the proteins that interact in the complex, and predict their structure. Lab 1 aims to train interdisciplinary students in these techniques using new tools in MS and bioinformatics. This novel laboratory course contains a mix of training and research objectives. Students will be trained in the use of MS protocols and tools, including several that have recently been developed by investigators at UCSD, such as PepNovo, a de novo sequencing tool (Frank and Pevzner, Anal Chem 2005;15:964), InsPecT for fast accurate searching of known post-translational modifications (Tanner et al, Anal Chem 2005 in press), Blimp for lind search for unknown modifications (Tsur et al, submitted), and DEX protocols for quantifying amide exchange in regions of proteins (Hotchko et al, submitted). Students will gain hands-on experience in data collection and the use of these analysis tools. There will be three 2-week modules, after which trainees will do a research project.

 

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