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Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly‐available database
40 auth. G. Omenn, D. States, M. Adamski, T. Blackwell, R. Menon, H. Hermjakob, R. Apweiler, B. Haab, R. Simpson, J. Eddes, Eugene A. Kapp, R. Moritz, D. Chan, A. Rai, A. Admon, ... R. Aebersold, J. Eng, W. Hancock, S. Hefta, H. Meyer, Y. Paik, J. Yoo, P. Ping, J. Pounds, J. Adkins, X. Qian, Rong Wang, V. Wasinger, Chi‐Yue Wu, Xiaohang Zhao, R. Zeng, A. Archakov, A. Tsugita, Ilan Beer, A. Pandey, Michael R Pisano, P. Andrews, H. Tammen, D. Speicher, S. Hanash
HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, hepar…
HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate‐anti‐coagulated plasma; and (3) created a publicly‐available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty‐five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS‐MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS‐MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay‐based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs.
Published in Proteomics
78
 9 2005