Human Proteome Project

Last updated
Human Proteome Project
Content
DescriptionWhole-proteome characterization
Data types
captured		protein sequence, phosphorylation, acetylation, glycosylation
Organisms Homo sapiens
Contact
Research center Human Proteome Organization
Laboratoryvarious
Primary citation PMID   22398612
Access
Website www.thehpp.org
www.c-hpp.org
Web service URL NextProt 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.

Contents

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
4 Yu-Ju Chen Taiwan
5Peter HorvatovichNetherlands
6Christoph BorchersCanada
7Edward NiceAustralia, New Zealand
8Pengyuan YangChina
9Je-Yoel ChoSeoul, Korea
10Joshua LabaerUSA
11Jong Shin YooKorea
12 Ravi Sirdeshmukh India, Singapore, Taiwan, Thailand
13Young Ki PaikKorea
14Charles PineauFrance
15Gilberto B DomontBrazil
16Fernando CorralesSpain
17 Gilbert S. Omenn USA
18Alex ArchakovRussia
19György Marko-VargaSweden
20Siqiu LiuChina
21Albert SickmannGermany
22 Akhilesh Pandey USA
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.[ 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

Related Research Articles

<span class="mw-page-title-main">Proteome</span> Set of proteins that can be expressed by a genome, cell, tissue, or organism

The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of the proteome.

<span class="mw-page-title-main">Stable isotope labeling by amino acids in cell culture</span>

Stable isotope labeling by/with amino acids in cell culture (SILAC) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling. It is a popular method for quantitative proteomics.

<span class="mw-page-title-main">Ruedi Aebersold</span> Swiss biologist (born 1954)

Rudolf Aebersold is a Swiss biologist, regarded as a pioneer in the fields of proteomics and systems biology. He has primarily researched techniques for measuring proteins in complex samples, in many cases via mass spectrometry. Ruedi Aebersold is a professor of Systems biology at the Institute of Molecular Systems Biology (IMSB) in ETH Zurich. He was one of the founders of the Institute for Systems Biology in Seattle, Washington, United States where he previously had a research group.

<span class="mw-page-title-main">HDLBP</span> Protein-coding gene in the species Homo sapiens

Vigilin is a 110 kDa protein that in humans is encoded by the HDLBP gene.

<span class="mw-page-title-main">MARK3</span> Protein-coding gene in the species Homo sapiens

MAP/microtubule affinity-regulating kinase 3 is an enzyme that in humans is encoded by the MARK3 gene.

<span class="mw-page-title-main">IGHA2</span> Gene in the species Homo sapiens

Ig alpha-2 chain C region is a protein that in humans is encoded by the IGHA2 gene.

<span class="mw-page-title-main">HRC (gene)</span> Protein-coding gene in the species Homo sapiens

Sarcoplasmic reticulum histidine-rich calcium-binding protein is a protein that in humans is encoded by the HRC gene.

<span class="mw-page-title-main">Isobaric tag for relative and absolute quantitation</span>

Isobaric tags for relative and absolute quantitation (iTRAQ) is an isobaric labeling method used in quantitative proteomics by tandem mass spectrometry to determine the amount of proteins from different sources in a single experiment. It uses stable isotope labeled molecules that can be covalent bonded to the N-terminus and side chain amines of proteins.

The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate data comparison, exchange and verification.

<i>Molecular & Cellular Proteomics</i> Academic journal

Molecular & Cellular Proteomics is a monthly peer-reviewed scientific journal established in 2002 and published by the American Society for Biochemistry and Molecular Biology. It covers research on structural and functional properties of proteins, especially with regard to development.

The PRIDE is a public data repository of mass spectrometry (MS) based proteomics data, and is maintained by the European Bioinformatics Institute as part of the Proteomics Team.

<span class="mw-page-title-main">Ronald Beavis</span> Canadian protein biochemist

Ronald Charles Beavis is a Canadian protein biochemist, who has been involved in the application of mass spectrometry to protein primary structure, with applications in the fields of proteomics and analytical biochemistry. He has developed methods for measuring the identity and post-translational modification state of proteins obtained from biological samples using mass spectrometry. He is currently best known for developing new methods for analyzing proteomics data and applying the results of these methods to problems in computational biology.

Zeng Rong is a Chinese biochemist researching and developing technology for proteomics research. She is currently a professor at the Institute of Biochemistry and Cell Biology at the Shanghai Institutes for Biological Sciences.

Debasis Dash is an Indian computational biologist and chief scientist at the Institute of Genomics and Integrative Biology (IGIB). Known for his research on proteomics and Big Data and Artificial Intelligence studies, his studies have been documented by way of a number of articles and ResearchGate, an online repository of scientific articles has listed 120 of them. The Department of Biotechnology of the Government of India awarded him the National Bioscience Award for Career Development, one of the highest Indian science awards, for his contributions to biosciences, in 2014. He was appointed as the director of Institute of Life Sciences, Bhubaneswar on 18 May 2023.

Young-Ki Paik is the director of the Yonsei Proteome Research Center in Seoul, Korea. In 2009, he was chosen President of the Human Proteome Organization (HUPO).

Catherine E. Costello is the William Fairfield Warren distinguished professor in the department of biochemistry, Cell Biology and Genomics, and the director of the Center for Biomedical Mass Spectrometry at the Boston University School of Medicine.

Yu-Ju Chen is a Taiwanese proteomics research scientist, who leads international projects in proteogenomics.

Peipei Ping is an academic specializing in cardiac physiology, system biology and data science.

Ravi Sirdeshmukh is an Indian cancer biologist and proteomicist. He is a distinguished scientist and incumbent associate director of the Institute of Bioinformatics (IOB) in Bangalore, founding president of the Proteomics Society of India and senior research advisor at the Mazumdar Shaw Center for Translational Research (MSCTR) in Bangalore. He is also an elected member of the Council of Human Proteome Organization. He is most noted for his contributions in the Human Proteome Project where he served as the Group Leader for the countries like India, Singapore, Taiwan and Thailand. Sirdeshmukh is also an invited member of the Council of Asian Oceanean HUPO (AOHUPO).

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. 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.
  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)
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.