Advancing intact proteome separation for top-down and bottom-up mass spectrometry

Imagine what it would be like to obtain your own medical history from a single drop of blood. By analyzing protein molecules (responsible for carrying out practically all biochemical functions), a physician could diagnose the early onset of disease, and perhaps even prescribe treatments to prevent the illness, even before you get sick! This is the dream of PROTEOMICS, an emerging science that utilizes advanced analytical techniques to characterize extremely complex biological mixtures (several thousand proteins detected in a single experiment). Unfortunately, despite the remarkable advances made over the last decade or so, the dream of proteomics has not been fully realized. Like other problems in science, the key to understanding proteomics lies in the development of improved technologies, both to simplify and to standardize the protein analysis strategy. This is the focus of my current research proposal. Proteomics has seen explosive growth since the applicability of mass spectrometry to accelerate characterization of the sample. Modern proteomics laboratories couple mass spectrometry with a multitude of analytical technologies to achieve proper detection of the many protein components in the sample. With the requested funds from NSERC, I aim to understand and facilitate protein sample preparation which will enable mass spectrometry detection. Research emphasis is on two of the most challenging problems in proteome analysis: (1) quantitative analysis of low abundance proteins; (2) manipulation of intact proteins, within the context of the emerging field of top-down proteomics. I propose methods to facilitate the direct analysis of intact proteins by mass spectrometry, and enhance the separation of proteins to further improve their characterization. I also propose strategies, based on labelling proteins at the intact level, to enable quantitative proteome profiling. It is anticipated through these innovations that proteome profiling will become a routine procedure that can thus be brought into clinical practice in order to improve human health.