Human Plasma Proteome Project Data Central at PeptideAtlas

Welcome to the HUPO/HPPP Data Central, hosted at PeptideAtlas.

Project Overview

The Human Proteome Organization (HUPO) in 2003 launched an effort to combine results from the many labs around the world who were working on the human plasma proteome. This effort, the Human Plasma Proteome Project (HPPP), continues today and the PeptideAtlas is an integral part of that effort.

Phase I of the effort, completed in 2005, involved the collection of plasma proteomics results from 18 laboratories and resulted in a list of 3020 identified proteins identified with two or more peptides regardless of laboratory or specimen. (Omenn et al., Proteomics, 2005). Later that year, States et al. applied rigorous statistical approach to the same data, yielding a reduced set of 889 proteins with at least 95% confidence in protein identification. Also in that same year, the first Human Plasma PeptideAtlas was constructed from 28 datasets, 20 of them from PPP I. This atlas build contained 960 distinct proteins.

At this writing, Phase II of the project is underway. HPPP II involves the collection and analysis of raw data rather than processed data. A significant aspect of HPPP III is the establishment of a standard method for the submission of data to the ProteomeXchange consortium databases PRIDE, PeptideAtlas, and Tranche. It is the policy of HPPP II that all published plasma data be submitted to PRIDE, from which it will be stored in Tranche and incorporated into the PeptideAtlas. As of summer 2011, the submission system is still under development. In June 2011, a high confidence (FDR 1%) list of 1929 identified proteins derived from 91 experiments, including Phase I and II data, was published (Farrah, et al.) and made available in PeptideAtlas.

Data and Results

Related Publications

Human Plasma A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas, Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmstrom J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold RH - Molecular and Cellular Proteomics, 2011 Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins, Farrah T, Deutsch EW, Aebersold R - Serum/Plasma Proteomics, Methods in Molecular Biology, 2011 A high confidence, manually validated human blood plasma protein reference set, Schenk, GJ Schoenhals, G de Souza, M Mann - BMC Medical Genomics, 2008 Mapping the human plasma proteome by SCX-LC-IMS-MS, Plasencia, S Trimpin, S Naylor, DE Clemmer - Journal of the American Society for Mass Spectrometry, 2007

HPPP Many articles in a special issue of Proteomics, 2005, volume 5, pages 3223-3519 Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study, States et al. (2006) Nature Biotech. 24(3):333-338 Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics, Fermin et al. (2006), Genome Biology, 7, R35. Exploring the Human Plasma Proteome, Wiley, GS Omenn (ed), Dec 2006.

Human Plasma Proteome Project Documents

• Report to HUPO Council, 2007, including PPP Workshop at 6th HUPO Congress, Seoul, 7 Oct 2007