Human Plasma Proteome Project Data Central at PeptideAtlas

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

Project Overview Information

"During 2003-2005, the PPP prepared and distributed reference specimens of human serum and plasma to 55 participating laboratories worldwide, stimulated access to emerging technologies, and generated substantial datasets and integrated databases for proteins detectable and identifiable in human serum and plasma. Experimental protocols used combinations of depletion, fractionation, mass spectrometry, and immunoassay methods linked via search engines and annotation groups to gene and protein databases. We created a new human plasma proteome database and have developed recommendations for use in future studies with plasma and serum."
Read more at the HUPO/PPP project website.

Read the Omenn et.al. review, published in Proteomics (2005).

News

• Upcoming Human Plasma Proteome Project special update at the AACC workshop at US HUPO Meeting (Bethesda, MD, USA):
  Tuesday March 18, 7-10pm
  Presenting: Gil Omenn, Eric Deutsch

Data and Results

Data Products Omenn et.al. List of 3020 proteins identified with two or more peptides regardless of laboratory or specimen States et.al. List of 889 high confidence HPPP proteins A rigorous statistical approach devised to take into account the length of coding regions in genes and multiple hypothesis testing yielded a reduced set of 889 proteins with at least 95% confidence in protein identification.

Raw and Processed Data U.Michigan Raw data here (slow!) and here (auth. required). Tranche Download available data from the Tranche repository PeptideAtlas Raw and processed data are available from the PeptideAtlas HPPP Data Repository PeptideAtlas build results for human plasma are available from Human Plasma Builds PRIDE Individual experiment results from several labs are available from PRIDE

Related Publications

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