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

Abstract

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-anticoagulated 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 multi- 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.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-positive 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.

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“…The Plasma Proteome Database comprises the collated quantitative data for 10 546 proteins that have been detected in plasma and serum using immunoassays or mass spectrometric techniques (http://www.plasmaproteomedatabase.org/) 25. A comparison of the NAF profile with the plasma proteome identified 1578 proteins in common (Fig.…”

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“…It may well be that such a practice will help exclude discrepancies in the literature data [2] and, in our opinion, will compel the contributors to adhere to the criteria used by the editors of PROTEOMICS when assessing submissions [3].…”

“…Unfortunately, despite the impressive advances made, primarily, within the framework of the international project "Human Proteome" [2], proteomics has not justified many hopes it had initially inspired. The current situation is perfectly characterized as "we began to run before we could walk" [3].…”

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“…By comparison, major issues remain in the identification of proteins from large-scale, automated experiments that analyse proteins via LC-MS/MS or LC-LC-MS/MS. Nonsystematic use of scoring cutoffs, that assess the number of peptides matching a protein and/or the quality of the match, can dramatically change the numbers of proteins deemed to have been identified from a complex sample [26,27]. In some cases, protein identities are made on the basis of a match between one fragmented peptide and a database entry.…”