Human Proteome Project Explained

Human Proteome Project
Description:Whole-proteome characterization
Scope:protein sequence, phosphorylation, acetylation, glycosylation
Organism:Homo sapiens
Center:Human Proteome Organization
Laboratory:various
Pmid:22398612
Url:

The Human Proteome Project[1] (HPP) is a collaborative effort coordinated by the Human Proteome Organization.[2] Its stated goal is to experimentally observe all of the proteins produced by the sequences translated from the human genome.

History

The Human Proteome Organization has served as a coordinating body for many long-running proteomics research projects associated with specific human tissues of clinical interest, such as blood plasma,[3] liver,[4] brain[5] and urine.[6] It has also been responsible for projects associated with specific technology [7] and standards [8] necessary for the large scale study of proteins.

The structure and goals of a larger project that would parallel the Human Genome Project has been debated in the scientific literature.[9] [10] [11] [12] [13] The results of this debate and a series of meetings at the World Congresses of the Human Proteome Organization in 2009, 2010 and 2011 has been the decision to define the Human Proteome Project as being composed of two sub-projects, C-HPP and B/D-HPP.[14] The C-HPP will be organized into 25 groups, one per human chromosome. The B/D-HPP will be organized into groups by the biological and disease relevance of proteins.[15]

Projects and groups

The current set of working groups are listed below, in order of the chromosome to be studied.

ChromosomeGroup leaderNational affiliation
1Ping XuChina
2Lydie LaneSwitzerland
3Takeshi KawamuraJapan
4Yu-Ju ChenTaiwan
5Peter HorvatovichNetherlands
6Christoph BorchersCanada
7Edward NiceAustralia, New Zealand
8Pengyuan YangChina
9Je-Yoel ChoSeoul, Korea
10Joshua LabaerUSA
11Jong Shin YooKorea
12Ravi SirdeshmukhIndia, Singapore, Taiwan, Thailand
13Young Ki PaikKorea
14Charles PineauFrance
15Gilberto B DomontBrazil
16Fernando CorralesSpain
17Gilbert S. OmennUSA
18Alex ArchakovRussia
19György Marko-VargaSweden
20Siqiu LiuChina
21Albert SickmannGermany
22Akhilesh PandeyUSA
XYasushi IshihamaJapan
YGhasem Hosseini SalekdehIran
MTAndrea UrbaniItaly

Computational resources

Data reduction, analysis and validation of MS/MS based proteomics results is being provided by Eric Deutsch at the Institute for Systems Biology, Seattle, USA (PeptideAtlas). Data handling associated with antibody methods is being coordinated by Kalle von Feilitzen, Stockholm, Sweden (Human Protein Atlas). Overall integration and reporting informatics are the responsibility of Lydie Lane at SIB, Geneva, Switzerland (NeXtProt). All data generated as part of HPP contributions are deposited to one of the ProteomeXchange repositories.

Current status

Updates on the Human Proteome Project are regularly published, e.g. in the Journal of Proteome Research (2014).[16] Metrics for the level of confidence associated with protein observations have been published[17] as has been a "MissingProteinPedia".[18] [19]

Based on a comparison of nine major annotation portals gave a spread of human protein counts from 21,819 to 18,891 (as of 2017).[20] The 2021 Metrics of the HPP show that protein expression has now been credibly detected 92.8% of the predicted proteins coded in the human genome.[21]

See also

External links

  1. HPP project page (www.hupo.org)
  2. HPP web site (www.thehpp.org)
  3. Chromosome-centric HPP web site (www.c-hpp.org)
  4. BD HPP web site (www.hupo.org/B/D-HPP)

Notes and References

  1. Legrain. P.. Aebersold. Rued. Kumar. Bala. Beretta. Laura. Costello. Catherine E.. Borchers. Christoph H.. Corthals . Garry L.. 29 April 2011. The Human Proteome Project: Current State and Future Direction. Molecular & Cellular Proteomics. 10. 7. M111.009993 . 10.1074/mcp.M111.009993. free . 21742803 . 3134076 .
  2. American Society for Biochemistry and Molecular Biology. HUPO (Human Proteome Organization) 1st World Congress. Mol Cell Proteomics. 9. 651–752. September 2002. 9 . 12474872 .
  3. Omenn . Gilbert S. . States . David J. . Adamski . Marcin . Blackwell . Thomas W. . Menon . Rajasree . Hermjakob . Henning . Apweiler . Rolf . Haab . Brian B. . Simpson . Richard J. . Eddes . James S. . Kapp . Eugene A. . Moritz . Robert L. . Chan . Daniel W. . Rai . Alex J. . Admon . Arie . August 2005 . Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database . Proteomics . 5 . 13 . 3226–3245 . 10.1002/pmic.200500358 . 1615-9853 . 16104056. 2718659 . 2027.42/86605 . free .
  4. He . Fuchu . December 2005 . Human liver proteome project: plan, progress, and perspectives . Molecular & Cellular Proteomics . 4 . 12 . 1841–1848 . 10.1074/mcp.R500013-MCP200 . free . 1535-9476 . 16118399. 34735692 .
  5. Hamacher . Michael . Stephan . Christian . Hardt . Tanja . Eisenacher . Martin . Henkel . Andreas . Wiltfang . Jens . Jimenez . Connie R. . Park . Young Mok . Marcus . Katrin . Meyer . Helmut E. . May 2008 . Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea . Proteomics . 8 . 9 . 1750–1753 . 10.1002/pmic.200701120 . 1615-9861 . 18384107. 20622786 .
  6. Yamamoto . Tadashi . Langham . Robyn G. . Ronco . Pierre . Knepper . Mark A. . Thongboonkerd . Visith . June 2008 . Towards standard protocols and guidelines for urine proteomics: a report on the Human Kidney and Urine Proteome Project (HKUPP) symposium and workshop, 6 October 2007, Seoul, Korea and 1 November 2007, San Francisco, CA, USA . Proteomics . 8 . 11 . 2156–2159 . 10.1002/pmic.200800138 . 1615-9861 . 18528840. 13764796 .
  7. Uhlen . Mathias . Ponten . Fredrik . April 2005 . Antibody-based proteomics for human tissue profiling . Molecular & Cellular Proteomics . 4 . 4 . 384–393 . 10.1074/mcp.R500009-MCP200 . 1535-9476 . 15695805. 16391377 . free .
  8. Orchard . Sandra . Taylor . Chris . Hermjakob . Henning . Zhu . Weimin . Julian . Randall . Apweiler . Rolf . August 2004 . Current status of proteomic standards development . Expert Review of Proteomics . 1 . 2 . 179–183 . 10.1586/14789450.1.2.179 . 1744-8387 . 15966812. 21359913 .
  9. Archakov . Alexander . Bergeron . John J. M. . Khlunov . Alexander . Lisitsa . Andrey . Paik . Young-Ki . September 2009 . The Moscow HUPO Human Proteome Project workshop . Molecular & Cellular Proteomics . 8 . 9 . 2199–2200 . 10.1074/mcp.H900009-MCP200 . free . 1535-9484 . 2742447 . 19734150.
  10. Baker . Mark S. . December 2009 . Building the 'practical' human proteome project - the next big thing in basic and clinical proteomics . Current Opinion in Molecular Therapeutics . 11 . 6 . 600–602 . 2040-3445 . 20077630.
  11. September 2010 . The call of the human proteome . Nature Methods . 7 . 9 . 661 . 10.1038/nmeth0910-661 . 1548-7105 . 20827799. 41368976 . free .
  12. Rabilloud . Thierry . Hochstrasser . Denis . Simpson . Richard J. . September 2010 . Is a gene-centric human proteome project the best way for proteomics to serve biology? . Proteomics . 10 . 17 . 3067–3072 . 10.1002/pmic.201000220 . 1615-9861 . 20648483. 1007.5378 . 14253657 .
  13. February 2010 . A gene-centric human proteome project: HUPO--the Human Proteome organization . Molecular & Cellular Proteomics . 9 . 2 . 427–429 . 10.1074/mcp.H900001-MCP200 . free . 1535-9484 . 2830851 . 20124355.
  14. Paik . Young-Ki . Jeong . Seul-Ki . Omenn . Gilbert S. . Uhlen . Mathias . Hanash . Samir . Cho . Sang Yun . Lee . Hyoung-Joo . Na . Keun . Choi . Eun-Young . Yan . Fangfei . Zhang . Fan . Zhang . Yue . Snyder . Michael . Cheng . Yong . Chen . Rui . 2012-03-07 . The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome . Nature Biotechnology . 30 . 3 . 221–223 . 10.1038/nbt.2152 . 1546-1696 . 22398612. 205276763 .
  15. Aebersold . Ruedi . Bader . Gary D. . Edwards . Aled M. . van Eyk . Jennifer E. . Kussmann . Martin . Qin . Jun . Omenn . Gilbert S. . 2013-01-04 . The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community . Journal of Proteome Research . 12 . 1 . 23–27 . 10.1021/pr301151m . 1535-3907 . 23259511.
  16. Paik . Young-Ki . Omenn . Gilbert S. . Thongboonkerd . Visith . Marko-Varga . Gyorgy . Hancock . William S. . 2014-01-03 . Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II . Journal of Proteome Research . 13 . 1 . 1–4 . 10.1021/pr4011958 . 1535-3907 . 24328071.
  17. Omenn . Gilbert S. . Lane . Lydie . Lundberg . Emma K. . Beavis . Ronald C. . Nesvizhskii . Alexey I. . Deutsch . Eric W. . 2015-09-04 . Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification . Journal of Proteome Research . 14 . 9 . 3452–3460 . 10.1021/acs.jproteome.5b00499 . 1535-3907 . 4755311 . 26155816.
  18. Horvatovich . Péter . Lundberg . Emma K. . Chen . Yu-Ju . Sung . Ting-Yi . He . Fuchu . Nice . Edouard C. . Goode . Robert J. . Yu . Simon . Ranganathan . Shoba . Baker . Mark S. . Domont . Gilberto B. . Velasquez . Erika . Li . Dong . Liu . Siqi . Wang . Quanhui . 2015-09-04 . Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project . Journal of Proteome Research . 14 . 9 . 3415–3431 . 10.1021/pr5013009 . 1535-3907 . 26076068.
  19. Baker . Mark S. . Ahn . Seong Beom . Mohamedali . Abidali . Islam . Mohammad T. . Cantor . David . Verhaert . Peter D. . Fanayan . Susan . Sharma . Samridhi . Nice . Edouard C. . Connor . Mark . Ranganathan . Shoba . 2017-01-24 . Accelerating the search for the missing proteins in the human proteome . Nature Communications . 8 . 14271 . 10.1038/ncomms14271 . 2041-1723 . 5286205 . 28117396. 2017NatCo...814271B .
  20. Southan . Christopher . 2017 . Last rolls of the yoyo: Assessing the human canonical protein count . F1000Research . 6 . 448 . 10.12688/f1000research.11119.1 . 2046-1402 . 5428527 . 28529709 . free .
  21. Omenn . Gilbert S. . Lane . Lydie . Overall . Christopher M. . Paik . Young-Ki . Cristea . Ileana M. . Corrales . Fernando J. . Lindskog . Cecilia . Weintraub . Susan . Roehrl . Michael H. A. . Liu . Siqi . Bandeira . Nuno . Srivastava . Sudhir . Chen . Yu-Ju . Aebersold . Ruedi . Moritz . Robert L. . Deutsch . Eric W. . Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project . Journal of Proteome Research . 3 December 2021 . 20 . 12 . 5227–5240 . 10.1021/acs.jproteome.1c00590. 34670092 . 9340669 . 239050778 .

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