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.
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.
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]
A review of nine major annotation portals gave a spread of human protein counts from 18,891 to 21,819 (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]
↑ 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. ISSN1615-9853. PMID16104056. S2CID2718659.
↑ 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. ISSN1615-9861. PMID18384107. S2CID20622786.
↑ 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. ISSN1615-9861. PMID18528840. S2CID13764796.
↑ 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. ISSN2040-3445. PMID20077630.
↑ 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. ISSN1546-1696. PMID22398612. S2CID205276763.
↑ 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. ISSN1535-3907. PMID23259511.
↑ 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. ISSN1535-3907. PMID24328071.
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