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Its pilot phase has (1)\u2005evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2)\u2005compared PPP reference specimens of human serum and EDTA, heparin, and citrate\u2010anti\u2010coagulated plasma; and (3)\u2005created a publicly\u2010available knowledge base (www.bioinformatics.med.umich.edu\/hupo\/ppp; www.ebi.ac.uk\/pride). Thirty\u2010five participating laboratories in 13\u2009countries submitted datasets. Working groups addressed (a)\u2005specimen stability and protein concentrations; (b)\u2005protein identifications from 18\u2005MS\/MS datasets; (c)\u2005independent analyses from raw MS\u2010MS spectra; (d)\u2005search engine performance, subproteome analyses, and biological insights; (e)\u2005antibody arrays; and (f)\u2005direct MS\/SELDI analyses. MS\u2010MS datasets had 15 710\u2009different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504\u2005IPI\u2005proteins identified with one or more peptides and 3020\u2009proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay\u2010based concentration determinations. The database permits examination of many other subsets, such as 1274\u2009proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs.<\/jats:p><jats:p>We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS\/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches.<\/jats:p><jats:p>This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false\u2010positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.<\/jats:p>","DOI":"10.1002\/pmic.200500358","type":"journal-article","created":{"date-parts":[[2005,8,16]],"date-time":"2005-08-16T07:49:53Z","timestamp":1124178593000},"page":"3226-3245","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":670,"title":["Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35\u2009collaborating laboratories and multiple analytical groups, generating a core dataset of 3020\u2009proteins and a publicly\u2010available 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