A high-stringency blueprint of the human proteome

Nat Commun. 2020 Oct 16;11(1):5301. doi: 10.1038/s41467-020-19045-9.

Authors

Subash Adhikari¹, Edouard C Nice^{1

2}, Eric W Deutsch³, Lydie Lane⁴, Gilbert S Omenn⁵, Stephen R Pennington⁶, Young-Ki Paik⁷, Christopher M Overall⁸, Fernando J Corrales⁹, Ileana M Cristea¹⁰, Jennifer E Van Eyk¹¹, Mathias Uhlén¹², Cecilia Lindskog¹³, Daniel W Chan¹⁴, Amos Bairoch⁴, James C Waddington⁶, Joshua L Justice¹⁰, Joshua LaBaer¹⁵, Henry Rodriguez¹⁶, Fuchu He¹⁷, Markus Kostrzewa¹⁸, Peipei Ping¹⁹, Rebekah L Gundry²⁰, Peter Stewart²¹, Sanjeeva Srivastava²², Sudhir Srivastava²³, Fabio C S Nogueira²⁴, Gilberto B Domont²⁴, Yves Vandenbrouck²⁵, Maggie P Y Lam^{26

27}, Sara Wennersten²⁸, Juan Antonio Vizcaino²⁹, Marc Wilkins³⁰, Jochen M Schwenk¹², Emma Lundberg¹², Nuno Bandeira³¹, Gyorgy Marko-Varga³², Susan T Weintraub³³, Charles Pineau³⁴, Ulrike Kusebauch³, Robert L Moritz³, Seong Beom Ahn¹, Magnus Palmblad³⁵, Michael P Snyder³⁶, Ruedi Aebersold^{3

37}, Mark S Baker^{38

39}

Affiliations

¹ Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
² Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia.
³ Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA.
⁴ Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland.
⁵ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA.
⁶ UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland.
⁷ Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea.
⁸ Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada.
⁹ Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain.
¹⁰ Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
¹¹ Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA.
¹² Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden.
¹³ Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden.
¹⁴ Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA.
¹⁵ Biodesign Institute, Arizona State University, Tempe, AZ, USA.
¹⁶ Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
¹⁷ State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
¹⁸ Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany.
¹⁹ Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
²⁰ CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
²¹ Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.
²² Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
²³ Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA.
²⁴ Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil.
²⁵ University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France.
²⁶ Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA.
²⁷ Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA.
²⁸ Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA.
²⁹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
³⁰ School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
³¹ Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA.
³² Department of Biomedical Engineering, Lund University, Lund, Sweden.
³³ Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA.
³⁴ University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France.
³⁵ Leiden University Medical Center, Leiden, 2333, The Netherlands.
³⁶ Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
³⁷ Faculty of Science, University of Zurich, Zurich, Switzerland.
³⁸ Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia. mark.baker@mq.edu.au.
³⁹ Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA. mark.baker@mq.edu.au.

Abstract

The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Disease / genetics*
Human Genome Project
Humans
Proteome / chemistry
Proteome / genetics*
Proteome / metabolism
Proteomics

Substances

Proteome

Abstract

Publication types

MeSH terms

Substances

Grants and funding