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
Laboratory various
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
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
17 Gilbert S. Omenn USA
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

Related Research Articles

Proteome 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.

Proteomics Large-scale study of proteins

Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions, for example composing the structural fibers of muscle to the enzymes that catalyze the digestion of food to synthesizing and replicating DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body.

Omics Suffix in biology

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Protein isoform Forms of a protein produced from different genes

A protein isoform, or "protein variant", is a member of a set of highly similar proteins that originate from a single gene or gene family and are the result of genetic differences. While many perform the same or similar biological roles, some isoforms have unique functions. A set of protein isoforms may be formed from alternative splicings, variable promoter usage, or other post-transcriptional modifications of a single gene; post-translational modifications are generally not considered. Through RNA splicing mechanisms, mRNA has the ability to select different protein-coding segments (exons) of a gene, or even different parts of exons from RNA to form different mRNA sequences. Each unique sequence produces a specific form of a protein.

Cathepsin O Protein-coding gene in the species Homo sapiens

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Ruedi Aebersold Swiss biologist, regarded as a pioneer (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, where he previously had a research group.

AMELY Protein-coding gene in the species Homo sapiens

Amelogenin, Y isoform is a protein that in humans is encoded by the AMELY gene. AMELY is located on the Y chromosome and encodes a form of amelogenin. Amelogenin is an extracellular matrix protein involved in biomineralization during tooth enamel development.

The Human Proteome Organization (HUPO) is an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. The organization was founded in June 2001 and it promotes the development and awareness of proteomics research, advocates on behalf of proteomics researchers throughout the world, and facilitates scientific collaborations between members and initiatives. Ultimately, it is organized to gain a better and more complete understanding of the human proteome.

PCTK3 Protein-coding gene in the species Homo sapiens

Serine/threonine-protein kinase PCTAIRE-3 is an enzyme that in humans is encoded by the PCTK3 gene.

DDX56 Protein-coding gene in the species Homo sapiens

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ATP1B3 Protein-coding gene in the species Homo sapiens

Sodium/potassium-transporting ATPase subunit beta-3 is an enzyme that in humans is encoded by the ATP1B3 gene. ATP1B3 has also been designated as CD298.

Probable ribosome biogenesis protein RLP24

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In proteomics, GPM stands for "Global Proteome Machine". It is a web-based, open source user interface for analyzing and displaying protein identification data. It was originally designed by Rob Craig and Ron Beavis and first released in 2003. The interface creates a series of web browser page views of tandem mass spectrometry data that has been assigned to protein sequences. The underlying data documents are stored in BIOML format files.

Marc R. Wilkins is an Australian scientist who is credited with the defining the concept of the proteome. Wilkins is a Professor in the School of Biotechnology and Biomolecular Sciences at the University of New South Wales, Sydney.

The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. In November 2021, version 21 was launched. A lot of new data and content have been added and the resource now includes ten separate sections with complementary information about all human proteins. All data has been updated on the approximately 15 million individual web pages. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and was selected by the organization ELIXIR as a European core resource due to its fundamental importance for a wider life science community. The HPA consortium is funded by the Knut and Alice Wallenberg Foundation.

Ronald Beavis 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.

Mathias Uhlén is a Swedish biologist, biotechnologist, and Professor of Microbiology at Royal Institute of Technology (KTH), Stockholm. His research interests cover antibody engineering, proteomics and precision medicine.

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.

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 . American Society for Biochemistry and Molecular Biology. 9 (9): 651–752. September 2002. PMID   12474872.{{cite journal}}: CS1 maint: url-status (link)
  3. ↑ Omenn, G.S. et al. Overview of the HUPO Plasma Proteome Project. Proteomics. 5, 3226-45 (2005).
  4. ↑ He, F. Human liver proteome project: plan, progress, and perspectives. Mol Cell Proteomics. 4, 1841-8 (2005).
  5. ↑ Hamacher, M. et al. HUPO Brain Proteome Project: toward a code of conduct. Mol Cell Proteomics. 7, 457 (2008).
  6. ↑ Yamamoto, T., Langham, R.G., Ronco, P., Knepper, M.A. & Thongboonkerd, V. Towards standard protocols and guidelines for urine proteomics. Proteomics. 8, 2156-9 (2008).
  7. ↑ Uhlen, M. & Ponten, F. Antibody-based proteomics for human tissue profiling. Mol Cell Proteomics. 4, 384-93 (2005).
  8. ↑ Orchard, S. et al. Current status of proteomic standards development. Expert Rev Proteomics. 1, 179-83 (2005).
  9. ↑ Archakov A, et al. The Moscow HUPO Human Proteome Project workshop. Mol Cell Proteomics. 8:2199-200 (2009).
  10. ↑ Baker MS. Building the 'practical' human proteome project - the next big thing in basic and clinical proteomics. Curr Opin Mol Ther. 2009 11:600-2 (2009).
  11. ↑ Editorial, The call of the human proteome. Nat Methods. 7:661 (2010).
  12. ↑ Rabilloud T., et al. Is a gene-centric human proteome project the best way for proteomics to serve biology? Proteomics. 10:3067-72 (2010).
  13. ↑ Editorial. A Gene-centric Human Proteome Project. Mol Cell Proteomics. 9:427-429 (2010).
  14. ↑ Paik, Y-K., et al. A Chromosome-Centric Human Proteome Project to Characterize the Sets of Proteins Encoded in the Genome. Nature Biotech.30: 221–3(2012).
  15. ↑ Aebersold R., et al. The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community. J. Proteome Res. 12:23–27 (2013).
  16. ↑ Paik Y-K., et al. Genome-wide Proteomics, Chromosome-centric Human Proteome Project (C-HPP), Part II. J. Proteome Res. 13:1–4 (2014).
  17. ↑ Omenn GS., et al. Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J Proteome Res. 14:3452-60 (2015).
  18. ↑ Horvatovich P., et al. A Quest for Missing Proteins: update 2015 on Chromosome-Centric Human Proteome Project. J Proteome Res. Jun 15 (2015).
  19. ↑ Baker, MS; et al. (2017). "Accelerating the search for the missing proteins in the human proteome". Nature Communications. 8: 14271. Bibcode:2017NatCo...814271B. doi:10.1038/ncomms14271. PMC   5286205 . PMID   28117396.
  20. ↑ Southan, Christopher (2017-04-07). "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. 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)
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