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Human Proteome Project

April 18, 2024

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.

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

History edit

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 edit

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 edit

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 edit

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 edit

References edit

  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.

External links 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)

April 18, 2024
human, proteome, project, collaborative, effort, coordinated, human, proteome, organization, stated, goal, experimentally, observe, proteins, produced, sequences, translated, from, human, genome, contentdescriptionwhole, proteome, characterizationdata, typesca. 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 Human Proteome ProjectContentDescriptionWhole proteome characterizationData typescapturedprotein sequence phosphorylation acetylation glycosylationOrganismsHomo sapiensContactResearch centerHuman Proteome OrganizationLaboratoryvariousPrimary citationPMID 22398612AccessWebsitewww wbr thehpp wbr org www wbr c hpp wbr orgWeb service URLNextProt REST Contents 1 History 2 Projects and groups 3 Computational resources 4 Current status 5 See also 6 References 7 External linksHistory editThe 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 editThe current set of working groups are listed below in order of the chromosome to be studied Chromosome Group leader National affiliation1 Ping Xu China2 Lydie Lane Switzerland3 Takeshi Kawamura Japan4 Yu Ju Chen Taiwan5 Peter Horvatovich Netherlands6 Christoph Borchers Canada7 Edward Nice Australia New Zealand8 Pengyuan Yang China9 Je Yoel Cho Seoul Korea10 Joshua Labaer USA11 Jong Shin Yoo Korea12 Ravi Sirdeshmukh India Singapore Taiwan Thailand13 Young Ki Paik Korea14 Charles Pineau France15 Gilberto B Domont Brazil16 Fernando Corrales Spain17 Gilbert S Omenn USA18 Alex Archakov Russia19 Gyorgy Marko Varga Sweden20 Siqiu Liu China21 Albert Sickmann Germany22 Akhilesh Pandey USAX Yasushi Ishihama JapanY Ghasem Hosseini Salekdeh IranMT Andrea Urbani ItalyComputational resources editData 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 editUpdates 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 editBioPlex Human Protein Atlas Protein databases NeXtProt PeptideAtlasReferences edit 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 amp 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 amp 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 18528840 S2CID 13764796 Uhlen Mathias Ponten Fredrik April 2005 Antibody based proteomics for human tissue profiling Molecular amp 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 amp 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 amp 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 1535 3907 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 1535 3907 PMC 4755311 PMID 26155816 Horvatovich Peter 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 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 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 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 External links editHPP 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 Retrieved from https en wikipedia org w index php title Human Proteome Project amp oldid 1216234576, wikipedia, wiki, book, books, library,

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