Human Proteome Project

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,{{Cite journal |last1=Omenn |first1=Gilbert S. |last2=States |first2=David J. |last3=Adamski |first3=Marcin |last4=Blackwell |first4=Thomas W. |last5=Menon |first5=Rajasree |last6=Hermjakob |first6=Henning |last7=Apweiler |first7=Rolf |last8=Haab |first8=Brian B. |last9=Simpson |first9=Richard J. |last10=Eddes |first10=James S. |last11=Kapp |first11=Eugene A. |last12=Moritz |first12=Robert L. |last13=Chan |first13=Daniel W. |last14=Rai |first14=Alex J. |last15=Admon |first15=Arie |date=August 2005 |title=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 |url=https://pubmed.ncbi.nlm.nih.gov/16104056/ |journal=Proteomics |volume=5 |issue=13 |pages=3226–3245 |doi=10.1002/pmic.200500358 |issn=1615-9853 |pmid=16104056|s2cid=2718659 |hdl=2027.42/86605 |hdl-access=free }} liver,{{Cite journal |last=He |first=Fuchu |date=December 2005 |title=Human liver proteome project: plan, progress, and perspectives |journal=Molecular & Cellular Proteomics |volume=4 |issue=12 |pages=1841–1848 |doi=10.1074/mcp.R500013-MCP200 |doi-access=free |issn=1535-9476 |pmid=16118399|s2cid=34735692 }} brain{{Cite journal |last1=Hamacher |first1=Michael |last2=Stephan |first2=Christian |last3=Hardt |first3=Tanja |last4=Eisenacher |first4=Martin |last5=Henkel |first5=Andreas |last6=Wiltfang |first6=Jens |last7=Jimenez |first7=Connie R. |last8=Park |first8=Young Mok |last9=Marcus |first9=Katrin |last10=Meyer |first10=Helmut E. |date=May 2008 |title=Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea |url=https://pubmed.ncbi.nlm.nih.gov/18384107/ |journal=Proteomics |volume=8 |issue=9 |pages=1750–1753 |doi=10.1002/pmic.200701120 |issn=1615-9861 |pmid=18384107|s2cid=20622786 }} and urine.{{Cite journal |last1=Yamamoto |first1=Tadashi |last2=Langham |first2=Robyn G. |last3=Ronco |first3=Pierre |last4=Knepper |first4=Mark A. |last5=Thongboonkerd |first5=Visith |date=June 2008 |title=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 |url=https://pubmed.ncbi.nlm.nih.gov/18528840/ |journal=Proteomics |volume=8 |issue=11 |pages=2156–2159 |doi=10.1002/pmic.200800138 |issn=1615-9861 |pmid=18528840|s2cid=13764796 }} It has also been responsible for projects associated with specific technology {{Cite journal |last1=Uhlen |first1=Mathias |last2=Ponten |first2=Fredrik |date=April 2005 |title=Antibody-based proteomics for human tissue profiling |journal=Molecular & Cellular Proteomics |volume=4 |issue=4 |pages=384–393 |doi=10.1074/mcp.R500009-MCP200 |issn=1535-9476 |pmid=15695805|s2cid=16391377 |doi-access=free }} and standards {{Cite journal |last1=Orchard |first1=Sandra |last2=Taylor |first2=Chris |last3=Hermjakob |first3=Henning |last4=Zhu |first4=Weimin |last5=Julian |first5=Randall |last6=Apweiler |first6=Rolf |date=August 2004 |title=Current status of proteomic standards development |url=https://pubmed.ncbi.nlm.nih.gov/15966812/ |journal=Expert Review of Proteomics |volume=1 |issue=2 |pages=179–183 |doi=10.1586/14789450.1.2.179 |issn=1744-8387 |pmid=15966812|s2cid=21359913 }} 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.{{Cite journal |last1=Archakov |first1=Alexander |last2=Bergeron |first2=John J. M. |last3=Khlunov |first3=Alexander |last4=Lisitsa |first4=Andrey |last5=Paik |first5=Young-Ki |date=September 2009 |title=The Moscow HUPO Human Proteome Project workshop |journal=Molecular & Cellular Proteomics |volume=8 |issue=9 |pages=2199–2200 |doi=10.1074/mcp.H900009-MCP200 |doi-access=free |issn=1535-9484 |pmc=2742447 |pmid=19734150}}{{Cite journal |last=Baker |first=Mark S. |date=December 2009 |title=Building the 'practical' human proteome project - the next big thing in basic and clinical proteomics |url=https://pubmed.ncbi.nlm.nih.gov/20077630/ |journal=Current Opinion in Molecular Therapeutics |volume=11 |issue=6 |pages=600–602 |issn=2040-3445 |pmid=20077630}}{{Cite journal |date=September 2010 |title=The call of the human proteome |journal=Nature Methods |volume=7 |issue=9 |pages=661 |doi=10.1038/nmeth0910-661 |issn=1548-7105 |pmid=20827799|s2cid=41368976 |doi-access=free }}{{Cite journal |last1=Rabilloud |first1=Thierry |last2=Hochstrasser |first2=Denis |last3=Simpson |first3=Richard J. |date=September 2010 |title=Is a gene-centric human proteome project the best way for proteomics to serve biology? |url=https://pubmed.ncbi.nlm.nih.gov/20648483/ |journal=Proteomics |volume=10 |issue=17 |pages=3067–3072 |doi=10.1002/pmic.201000220 |issn=1615-9861 |pmid=20648483|arxiv=1007.5378 |s2cid=14253657 }}{{Cite journal |date=February 2010 |title=A gene-centric human proteome project: HUPO--the Human Proteome organization |journal=Molecular & Cellular Proteomics |volume=9 |issue=2 |pages=427–429 |doi=10.1074/mcp.H900001-MCP200 |doi-access=free |issn=1535-9484 |pmc=2830851 |pmid=20124355}} 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.{{Cite journal |last1=Paik |first1=Young-Ki |last2=Jeong |first2=Seul-Ki |last3=Omenn |first3=Gilbert S. |last4=Uhlen |first4=Mathias |last5=Hanash |first5=Samir |last6=Cho |first6=Sang Yun |last7=Lee |first7=Hyoung-Joo |last8=Na |first8=Keun |last9=Choi |first9=Eun-Young |last10=Yan |first10=Fangfei |last11=Zhang |first11=Fan |last12=Zhang |first12=Yue |last13=Snyder |first13=Michael |last14=Cheng |first14=Yong |last15=Chen |first15=Rui |date=2012-03-07 |title=The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome |url=https://pubmed.ncbi.nlm.nih.gov/22398612/ |journal=Nature Biotechnology |volume=30 |issue=3 |pages=221–223 |doi=10.1038/nbt.2152 |issn=1546-1696 |pmid=22398612|s2cid=205276763 }} 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.{{Cite journal |last1=Aebersold |first1=Ruedi |last2=Bader |first2=Gary D. |last3=Edwards |first3=Aled M. |last4=van Eyk |first4=Jennifer E. |last5=Kussmann |first5=Martin |last6=Qin |first6=Jun |last7=Omenn |first7=Gilbert S. |date=2013-01-04 |title=The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community |url=https://pubmed.ncbi.nlm.nih.gov/23259511/ |journal=Journal of Proteome Research |volume=12 |issue=1 |pages=23–27 |doi=10.1021/pr301151m |issn=1535-3907 |pmid=23259511}}

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.{{cn|date=December 2023}}

Updates on the Human Proteome Project are regularly published, e.g. in the Journal of Proteome Research (2014).{{Cite journal |last1=Paik |first1=Young-Ki |last2=Omenn |first2=Gilbert S. |last3=Thongboonkerd |first3=Visith |last4=Marko-Varga |first4=Gyorgy |last5=Hancock |first5=William S. |date=2014-01-03 |title=Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II |url=https://pubmed.ncbi.nlm.nih.gov/24328071/ |journal=Journal of Proteome Research |volume=13 |issue=1 |pages=1–4 |doi=10.1021/pr4011958 |issn=1535-3907 |pmid=24328071}} Metrics for the level of confidence associated with protein observations have been published{{Cite journal |last1=Omenn |first1=Gilbert S. |last2=Lane |first2=Lydie |last3=Lundberg |first3=Emma K. |last4=Beavis |first4=Ronald C. |last5=Nesvizhskii |first5=Alexey I. |last6=Deutsch |first6=Eric W. |date=2015-09-04 |title=Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification |journal=Journal of Proteome Research |volume=14 |issue=9 |pages=3452–3460 |doi=10.1021/acs.jproteome.5b00499 |issn=1535-3907 |pmc=4755311 |pmid=26155816}} as has been a "MissingProteinPedia".{{Cite journal |last1=Horvatovich |first1=Péter |last2=Lundberg |first2=Emma K. |last3=Chen |first3=Yu-Ju |last4=Sung |first4=Ting-Yi |last5=He |first5=Fuchu |last6=Nice |first6=Edouard C. |last7=Goode |first7=Robert J. |last8=Yu |first8=Simon |last9=Ranganathan |first9=Shoba |last10=Baker |first10=Mark S. |last11=Domont |first11=Gilberto B. |last12=Velasquez |first12=Erika |last13=Li |first13=Dong |last14=Liu |first14=Siqi |last15=Wang |first15=Quanhui |date=2015-09-04 |title=Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project |url=https://pure.rug.nl/ws/files/82948510/A_Quest_for_Missing_Proteins_update_2015_on_Chromosome_Centric_Human_Proteome.pdf |journal=Journal of Proteome Research |volume=14 |issue=9 |pages=3415–3431 |doi=10.1021/pr5013009 |issn=1535-3907 |pmid=26076068}}{{Cite journal |last1=Baker |first1=Mark S. |last2=Ahn |first2=Seong Beom |last3=Mohamedali |first3=Abidali |last4=Islam |first4=Mohammad T. |last5=Cantor |first5=David |last6=Verhaert |first6=Peter D. |last7=Fanayan |first7=Susan |last8=Sharma |first8=Samridhi |last9=Nice |first9=Edouard C. |last10=Connor |first10=Mark |last11=Ranganathan |first11=Shoba |date=2017-01-24 |title=Accelerating the search for the missing proteins in the human proteome |journal=Nature Communications |volume=8 |pages=14271 |doi=10.1038/ncomms14271 |issn=2041-1723 |pmc=5286205 |pmid=28117396|bibcode=2017NatCo...814271B }}

A review of nine major annotation portals gave a spread of human protein counts from 18,891 to 21,819 (as of 2017).{{Cite journal |last=Southan |first=Christopher |date=2017 |title=Last rolls of the yoyo: Assessing the human canonical protein count |journal=F1000Research |volume=6 |pages=448 |doi=10.12688/f1000research.11119.1 |issn=2046-1402 |pmc=5428527 |pmid=28529709 |doi-access=free }} 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.{{cite journal |last1=Omenn |first1=Gilbert S. |last2=Lane |first2=Lydie |last3=Overall |first3=Christopher M. |last4=Paik |first4=Young-Ki |last5=Cristea |first5=Ileana M. |last6=Corrales |first6=Fernando J. |last7=Lindskog |first7=Cecilia |last8=Weintraub |first8=Susan |last9=Roehrl |first9=Michael H. A. |last10=Liu |first10=Siqi |last11=Bandeira |first11=Nuno |last12=Srivastava |first12=Sudhir |last13=Chen |first13=Yu-Ju |last14=Aebersold |first14=Ruedi |last15=Moritz |first15=Robert L. |last16=Deutsch |first16=Eric W. |title=Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project |journal=Journal of Proteome Research |date=3 December 2021 |volume=20 |issue=12 |pages=5227–5240 |doi=10.1021/acs.jproteome.1c00590|pmid=34670092 |pmc=9340669 |s2cid=239050778 }}

• BioPlex
• Human Protein Atlas - Protein databases
• NeXtProt
• PeptideAtlas
• Human Proteome Folding Project

{{Reflist|2}}

1. [http://www.hupo.org/human-proteome-project/ HPP project page (www.hupo.org)]
2. [http://www.thehpp.org/ HPP web site (www.thehpp.org)]
3. [http://www.c-hpp.org/ Chromosome-centric HPP web site (www.c-hpp.org)]
4. [https://www.hupo.org/B/D-HPP BD HPP web site (www.hupo.org/B/D-HPP)]

{{Genomics}}

Category:Proteomics

Category:Human genome projects

Category:Protein databases