Predoctoral Trainee

Shane Hubler Mathematics Graduate Program 616 Van Vleck Hall, E B 480 Lincoln Drive Faculty supervisor: George Craciun Email: hubler@math.wisc.edu (608) 263-2437

I am currently working with Dr. Gheorghe Craciun (Departments of Mathematics and Biomolecular Chemistry) and his collaborator, Dr. Joshua Coon (Departments of Chemistry and Biomolecular Chemistry) to develop de novo techniques in protein sequencing by analyzing mass spectrometry data. The goal of this research is to create a reliable pipeline that will identify peptide sequences directly from tandem mass spectrometry. The algorithm must perform equally well with well-known and new proteins.The same techniques should also apply regardless of complicating factors, such as phosphorylation or unusual chemical interactions.

Two kinds of data that can be used for input: low mass resolution and high mass resolution; recent developments in mass spectrometry have improved resolution and precision by more than three orders of magnitude. The algorithmic solutions to de novo sequences in these two cases may be different. For example, we have found that low resolution solutions can easily lead to combinatorial explosion; a very large number of possibilities arise with increased mass ambiguity. In addition to writing these algorithms, we will investigate how the accuracy affects the possible solutions.

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File last modified: August 13, 2003
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