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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

PeptideAtlas Raw and processed data are available from the PeptideAtlas HPPP Data Repository and a repository for the 91 experiments in Farrah, et al., 2011
PeptideAtlas build results for human plasma are available from Human Plasma Builds
PRIDE Download HPPP I results from several labs and HPPP II raw data from PRIDE.
Tranche Download available data directly from the Tranche repository

Related Publications

   Human Plasma



   HPPP



Human Plasma Proteome Project Documents



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