Abstract
The Human Proteomics Organization (HUPO) Human Plasma Proteome Project (PPP) is a prominent example of the inherently collaborative nature of the overall community effort to characterize the proteome of humans in health and disease. The PPP Pilot Phase, called "Exploring the Human Plasma Proteome", engaged 55 laboratories, four technical committees, and vendors and sponsors on an international scale. Among other outcomes, the PPP generated a Core Dataset of 3020 proteins identified with two or more peptides, fully accessible at EBI/PRIDE, ISB/PeptideAtlas, and University of Michigan websites, a rich resource for follow-on analyses. The PPP provided extensive annotation, correlation of number of peptides with protein concentrations measured by immunoassay, an algorithm for choice of a representative protein for multiple proteins matching a given peptide, and independent analyses from the raw spectra. The next phase of the PPP will emphasize standardized procedures for specimen handling, potent new technology platforms for discovery and for targeted proteomics, and robust informatics efforts, including comparative analyses of other biofluids.
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