Human proteome project

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

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.

Current status

The ongoing operations of the chromosome-based Human Proteome Project was the subject of a special issue of the Journal of Proteome Research (January 3, 2014, Volume 13, Issue 1). The status of the overall project was discussed in an Editorial in that issue.[16]

A separate CHPP-wiki has been established by the project's bioinformatics group to maintain current project information, including meetings, events, SOPs and other special resources for the individual chromosome teams.

Metrics for the level of confidence associated with protein observations are a key component of this project. How to define metrics that are meaningful for the variety of experimental protocols being used is a subject of ongoing debate: the current consensus metrics have been published.[17]

Journal articles describing recent status of the project and announcing the launch of the "MissingProteinPedia" can be found here.[18][19]

See also

References
  1. Legrain, P. et al. The human proteome project: Current state and future direction. Mol Cell Proteomics. 10:M111.009993 (2011).
  2. HUPO (Human Proteome Organization) 1st World Congress. Mol Cell Proteomics. 9:651-752 (2002).
  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. doi:10.1038/ncomms14271. PMC 5286205.
  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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