The scientific focus of our research is to understand the chemical basis for phenotype in photosynthetic organisms, with an emphasis on the immunity of plants and algae to infection. Our technical focus is on peptide mass spectrometry because we believe that proteotype is the proximal cause of phenotype (see Fig. 1). The proteotype is the complete, proteomic state of a cell or organism. We develop and apply methods to directly measure proteotypes of interest. By applying the algorithms and computational resources of systems biology to our proteome-wide datasets we discover mechanisms that regulate phenotype.
In collaboration with Prof. Vineet Bafna (Computer Science & Engineering, UC San Diego), we use peptide mass spectra to annotate the protein coding sequences of genomes. Peptide data provide an orthogonal complement to nucleic acid annotation. This approach is called proteogenomics; it has enabled us to discover, revise, or confirm tens of thousands of gene models.