Scientific project coordinated by the Human Proteome Organization
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.
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
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
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
References
^ 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 .
^
"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 .
^ 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 .
^ 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 .
^ 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 .
^ 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
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S2CID
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^ 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 .
^ 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 .
^ 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 .
^ 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 .
^
"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 .
^ 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 .
^
"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 .
^ 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 .
^ 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 .
^ 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
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PMID
24328071 .
^ 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
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PMC
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PMID
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^ 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
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PMID
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^ 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
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PMC
5286205 .
PMID
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^ Southan, Christopher (2017).
"Last rolls of the yoyo: Assessing the human canonical protein count" . F1000Research . 6 : 448.
doi :
10.12688/f1000research.11119.1 .
ISSN
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PMC
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PMID
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^ 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
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S2CID
239050778 .
External links
HPP project page (www.hupo.org)
HPP web site (www.thehpp.org)
Chromosome-centric HPP web site (www.c-hpp.org)
BD HPP web site (www.hupo.org/B/D-HPP)