Human Plasma Proteome Project Data Central at PeptideAtlas
Welcome to the HUPO/HPPP Data Central, hosted at PeptideAtlas.
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
et al.) and made available in PeptideAtlas.
Data and Results
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,
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
- 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