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Human Proteome Project

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Human Proteome Project
Content
DescriptionWhole-proteome characterization
Data types
captured		protein sequence, phosphorylation, acetylation, glycosylation
OrganismsHomo sapiens
Contact
Research centerHuman Proteome Organization
Laboratoryvarious
Primary citationPMID 22398612
Access
Websitewww.thehpp.org
www.c-hpp.org
Web service URLNextProt REST

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

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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

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

Chromosome Group leader National affiliation
1 Ping Xu China
2 Lydie Lane Switzerland
3 Takeshi Kawamura Japan
4 Yu-Ju Chen Taiwan
5 Peter Horvatovich Netherlands
6 Christoph Borchers Canada
7 Edward Nice Australia, New Zealand
8 Pengyuan Yang China
9 Je-Yoel Cho Seoul, Korea
10 Joshua Labaer USA
11 Jong Shin Yoo Korea
12 Ravi Sirdeshmukh India, Singapore, Taiwan, Thailand
13 Young Ki Paik Korea
14 Charles Pineau France
15 Gilberto B Domont Brazil
16 Fernando Corrales Spain
17 Gilbert S. Omenn USA
18 Alex Archakov Russia
19 György Marko-Varga Sweden
20 Siqiu Liu China
21 Albert Sickmann Germany
22 Akhilesh Pandey USA
X Yasushi Ishihama Japan
Y Ghasem Hosseini Salekdeh Iran
MT Andrea Urbani Italy

Computational resources

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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.[citation needed]

Current status

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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

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References

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  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. doi:10.1074/mcp.M111.009993. PMC 3134076. PMID 21742803.
  2. ^ "HUPO (Human Proteome Organization) 1st World Congress". Mol Cell Proteomics. 9 (9). American Society for Biochemistry and Molecular Biology: 651–752. September 2002. PMID 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. doi:10.1002/pmic.200500358. hdl:2027.42/86605. ISSN 1615-9853. PMID 16104056. S2CID 2718659.
  4. ^ He, Fuchu (December 2005). "Human liver proteome project: plan, progress, and perspectives". Molecular & Cellular Proteomics. 4 (12): 1841–1848. doi:10.1074/mcp.R500013-MCP200. ISSN 1535-9476. PMID 16118399. S2CID 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. doi:10.1002/pmic.200701120. ISSN 1615-9861. PMID 18384107. S2CID 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. doi:10.1002/pmic.200800138. ISSN 1615-9861. PMID 18528840. S2CID 13764796.
  7. ^ Uhlen, Mathias; Ponten, Fredrik (April 2005). "Antibody-based proteomics for human tissue profiling". Molecular & Cellular Proteomics. 4 (4): 384–393. doi:10.1074/mcp.R500009-MCP200. ISSN 1535-9476. PMID 15695805. S2CID 16391377.
  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. doi:10.1586/14789450.1.2.179. ISSN 1744-8387. PMID 15966812. S2CID 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. doi:10.1074/mcp.H900009-MCP200. ISSN 1535-9484. PMC 2742447. PMID 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. ISSN 2040-3445. PMID 20077630.
  11. ^ "The call of the human proteome". Nature Methods. 7 (9): 661. September 2010. doi:10.1038/nmeth0910-661. ISSN 1548-7105. PMID 20827799. S2CID 41368976.
  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. arXiv:1007.5378. doi:10.1002/pmic.201000220. ISSN 1615-9861. PMID 20648483. S2CID 14253657.
  13. ^ "A gene-centric human proteome project: HUPO--the Human Proteome organization". Molecular & Cellular Proteomics. 9 (2): 427–429. February 2010. doi:10.1074/mcp.H900001-MCP200. ISSN 1535-9484. PMC 2830851. PMID 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. doi:10.1038/nbt.2152. ISSN 1546-1696. PMID 22398612. S2CID 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. doi:10.1021/pr301151m. ISSN 1535-3907. PMID 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. doi:10.1021/pr4011958. ISSN 1535-3907. PMID 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. doi:10.1021/acs.jproteome.5b00499. ISSN 1535-3907. PMC 4755311. PMID 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" (PDF). Journal of Proteome Research. 14 (9): 3415–3431. doi:10.1021/pr5013009. ISSN 1535-3907. PMID 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. Bibcode:2017NatCo...814271B. doi:10.1038/ncomms14271. ISSN 2041-1723. PMC 5286205. PMID 28117396.
  20. ^ Southan, Christopher (2017). "Last rolls of the yoyo: Assessing the human canonical protein count". F1000Research. 6: 448. doi:10.12688/f1000research.11119.1. ISSN 2046-1402. PMC 5428527. PMID 28529709.
  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. (3 December 2021). "Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project". Journal of Proteome Research. 20 (12): 5227–5240. doi:10.1021/acs.jproteome.1c00590. PMC 9340669. PMID 34670092. S2CID 239050778.
[edit]
  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)
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