Technology drives biological research. A new technology can instantly provide answers that were difficult or impossible to address using current approaches. The emerging field of proteomics provides researchers an alternative/complementary strategy to the traditional genetic and biochemical approaches now used. Mass spectrometry is the enabling tool in proteomics and provides the ability to identify, characterize and even quantify differences at the protein level in cells and tissues. Landmark improvements in mass spectrometry-based proteomics allow for the comparative profiling of thousands of proteins in normal and disease states directly from complex mixtures (1). Finally, bioinformatics plays a major role in my lab to help fuel large-scale experiments (2).

One grant-funded project in the lab is to develop and apply methods for global phosphorylation analysis and quantification. We recently described a new approach to phosphorylation analysis where 2,002 sites of phosphorylation were detected on 900 proteins isolated from HeLa cell nuclei (3). We are now looking at cell cycle-specific phosphorylation events by profiling phosphorylation in synchronized yeast and HeLa cells.

A second major project in the lab is to develop mass spectrometry-based technologies to study protein ubiquitination. Ubiquitination is an extremely common posttranslational modification which in the past has been difficult to directly study because of the size of the modification (~8500 Da). In addition, polyubiquitin chains can be formed through either the traditional lysine 48 of ubiquitin or through any of six other alternative lysines present. A major goal of the lab is to unravel the biological function of each specific chain type using mass spectrometry and novel reagents called AQUA peptides (4).