Grant: Discovery Grants Program - Individual

The field of proteomics is growing rapidly and its impact in the biological sciences cannot be overstated. Major breakthroughs have been made in the last three years and have contributed significantly to our understanding of biological systems. However, despite major advances in mass spectrometry, separation sciences and bioinformatics there are still many challenges ahead, especially in the characterization of low abundance components and post-translational modifications.In this grant application, a number of solutions will be proposed to address these issues. These will included the chemical synthesis of libraries of well defined synthetic peptides corresponding to low abundance proteins that are typically difficult to detect with the current approaches. Several thousands peptides can be produced inexpensively and in sufficient amounts and purity for mass spec analysis. Their properties such as fragment ions and LC retention times will be extremely useful for a wide range of proteomics experiments both in the targeted mode (scheduled MRM) and in the discovery mode (""bottom-up"" proteomics). Peptides containing stable isotopes fro absolute quantitation, as well as peptides with chemical modifications will also be synthesize. These peptides and their properties will be submitted to the publicly available database in the Global Protein Machine (GPM) and used in the software PEAKS to increase confidence in assignment of peptides in LC MS/MS. In parallel we will also developed alternate new methods for ""top-down"" and ""medium -down"" sequencing that will provide for better characterization of post-translational modifications because either the intact proteins or larger protein fragments will be analyzed and fragmented in the mass spectrometer.Ultimately these new techniques will find applications in all areas of biological and biomedical research. These new approaches will allow for more comprehensive proteomics experiments and will be applied to complex biological systems such as in stem cells research as well as in clinical diagnostics.