Human proteome project

Human Proteome Project
Content
Description Whole-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
GPMDB 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.

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 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 Fuchu He China
2 Lydie Lane Switzerland
3 Toshihide Nishimura Japan
4 Yu Ju Chen Taiwan
5 Rainer Bischoff Netherlands
6 Paul Keown Canada
7 Ed Nice Australia, New Zealand
8 Pengyuan Yang China
9 Je-Yoel Cho Seoul, Korea
10 Joshua Labaer USA
11 Jong Shin Yoo Korea
12 Visith Thongboonkerd India, Singapore, Taiwan, Thailand
13 Young Ki Paik Korea
14 Jérôme Garin France
15 Gilberto B Domont Brazil
16 Fernando Corrales Spain
17 Bill Hancock USA
18 Alex Archakov Russia
19 Gyorgy Marko Varga Sweden
20 Siqiu Liu China
21 Daniel Figeys Canada
22 Charles Lee USA
X Tadashi Yamamoto Japan
Y Hosseini Salekdeh Iran
MT Andrea Urbani Italy

Computational resources

Data reduction, analysis and validation of MS/MS based proteomics results is being provided by Ron Beavis' group at the University of Manitoba, Winnipeg, CA (GPM,GPMDB) and Eric Deutsch's group 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). GPMDB makes its quarterly guide to identified human proteins available in several formats here.

Current status

The on-going 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]

A Journal article describing the most recent status of the project can be found here.[18]

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).

External links

  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.thehpp.org/BD-HPP.php)
  5. Oct. 2012 Dataset Guidelines
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