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. The last PeptideAtlas build contained over 3000 distinct proteins.

The latest publication summarizing the state of the Human Plasma Proteome Project can be found at Advances and Utility of the Human Plasma Proteome, Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM, J Proteome Res. 2021 Dec 3;20(12):5241-5263

• A summary table of proteins identified in the build
• A table of all datasets that have gone into the build
• Direct access to browse the Plasma PeptideAtlas 2021 build
• Human Plasma PeptideAtlas

Related Publications

Human Plasma

• Advances and Utility of the Human Plasma Proteome, Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM, J Proteome Res. 2021 Dec 3;20(12):5241-5263
• The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays, Schwenk et al., Journal of Proteome Research, 2017
• 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