Abstract

Proteomic and Proteogenomic Approaches as a Platform for Investigating Human Diseases

T S Keshava Prasad, Scientist, Institute of Bioinformatics

Advancement of technologies in mass spectrometry-based proteomics for high-throughput characterization of proteins has renewed efforts to identify novel biomarkers of human diseases. Recent improvements in mass spectrometry allow researchers to accomplish unbiased analysis of the entire protein complement of cells or body fluids in a single experiment. Proteomic studies to identify differentially regulated proteins between disease and normal conditions are now common. Quantitative proteomic strategies such as SILAC (stable isotope labeling with amino acids in cell culture) and iTRAQ (isobaric tags for relative and absolute quantitation) have contributed immensely to our ability to accurately determine relative protein levels, which are being utilized for discovery of biomarkers of diseases. In addition to protein profiling studies, mass spectrometry is also being employed in the quantitative analysis of post-translational modifications such as phosphorylation, which can be used to dissect signaling pathways driving human diseases. It is possible today to identify and quantify proteome of an organism or a tissue to its entirety, which facilitated the use of proteomic data for the near complete annotation of newly sequenced genomes. As a result, a new area of science was born called – proteogenomics. Successful outcome of such analyses include identification of novel genes, novel exons, novel initiation codons, exon extensions, intronic genes and cSNPs. In recent times, we have initiated a systematic effort to apply proteogenomic concepts to annotate both sequenced and unsequenced genomes of organisms, which are important from health biomedical point of view. In this talk, I will share vignettes of how we used proteomic and proteogenomic platforms to investigate human diseases.