Pilot Phase Results of the Human Proteome Organization Plasma Proteome Project.

The protein components of blood play essential roles in coagulation, inflammation, immunity, growth and development. Recognizing the importance of blood proteins in health and disease, the Human Proteome Organization (http://www.hupo.org) chose the Plasma Proteome Project (PPP) as the first tissue specific analysis to be implemented. The PPP is a collaboration of more than 30 laboratories and research groups worldwide. The June 2004 PPP Jamboree held in Ann Arbor, MI marked the completion of the pilot phase of the PPP with more than 50,000 peptide identifications reported leading to a high confidence consensus list of about 2,300 human blood proteins. Important contributions of the pilot phase of the PPP include the identification of over 2 thousands human blood proteins, comparative assessment of proteomic analysis of serum and plasma prepared using citrate, EDTA and heparin anticoagulants samples prepared from a single well defined donor pool; assessment of abundant protein depletion technologies to enhance the dynamic range of proteome analysis; comparative assessment of different protein and peptide fractionation technologies; comparison of MALDI peptide fingerprinting, liquid chromatography electrospray tandem mass spectroscopy, direct MS/SELDI, and accurate mass tag strategies; correlation of protein abundance with success in mass spectroscopy identification; comparison of Sequest, Mascot, SpectrumMill and X!Tandem software for mass spectroscopy data analysis; comparison of NCBI NR, IPI and full 6-frame genome translation databases; establishing quality measures for the different software packages; establishing quality assurance and data validation protocols for large multi-center proteomics studies. These results demonstrate the potential for large scale proteome analysis as well as highlighting important challenges that lie ahead.