Painting a Moving Picture: Large-Scale Proteomics Efforts and Their Potential for Changing Patient Care

Many investigators have used proteomic methodologies to investigate specific questions in basic biology and medical science. Indeed, many millions of dollars have been spent around the world on the generation of extensive lists of proteins that reside in a particular organelle, cell type, tissue, or body fluid. These lists represent the proteomes of those specific systems. Many studies attempt to go one step further and compare proteomes via a variety of approaches, in most cases with methods that are much too imprecise to be considered for clinical use. Some argue that it is difficult to point to the clinical application of these lists and crude comparisons, but at least 2 organizations are aiming to lead or synthesize expanded efforts to characterize the human proteome (see the suggested reading in the Data Supplement that accompanies the online version of this Q&A at http://www.clinchem.org/content/vol57/issue10). What does this mean for clinical laboratory medicine? Can the results of these efforts possibly lead to important discoveries that will change how we care for our patients? We compiled the opinions of 4 experts in proteomics and genomics to provide a perspective from individual leading investigators and the National Human Genome Research Institute. Their views provide cautious optimism and important insights on how to move forward. In general, have experiments aimed at cataloguing human proteomes made important advances? N. Leigh Anderson: Yes. I would point to 3 significant results as examples: (1) the reliable detection of almost 2000 proteins in human plasma by numerous groups; (2) passing the halfway point in the Human Proteome Resource effort to use antibodies to map locations of the human proteins by Matthias Uhlen et al. (see suggested reading in the online Data Supplement); and (3) the recent synthesis and characterization of nearly all human tryptic proteotypic peptides by Robert Moritz, Ruedi …