A high-stringency blueprint of the human proteome

Subash Adhikari; Edouard C. Nice; Eric W. Deutsch; Lydie Lane; Gilbert S. Omenn; Stephen R. Pennington; Young Ki Paik; Christopher M. Overall; Fernando J. Corrales; Ileana M. Cristea; Jennifer E. Van Eyk; Mathias Uhlén; Cecilia Lindskog; Daniel W. Chan; Amos Bairoch; James C. Waddington; Joshua L. Justice; Joshua LaBaer; Henry Rodriguez; Fuchu He; Markus Kostrzewa; Peipei Ping; Rebekah L. Gundry; Peter Stewart; Sanjeeva Srivastava; Sudhir Srivastava; Fabio C.S. Nogueira; Gilberto B. Domont; Yves Vandenbrouck; Maggie P.Y. Lam; Sara Wennersten; Juan Antonio Vizcaino; Marc Wilkins; Jochen M. Schwenk; Emma Lundberg; Nuno Bandeira; Gyorgy Marko-Varga; Susan T. Weintraub; Charles Pineau; Ulrike Kusebauch; Robert L. Moritz; Seong Beom Ahn; Magnus Palmblad; Michael P. Snyder; Ruedi Aebersold; Mark S. Baker

doi:10.1038/s41467-020-19045-9

A high-stringency blueprint of the human proteome

Subash Adhikari, Edouard C. Nice, Eric W. Deutsch, Lydie Lane, Gilbert S. Omenn, Stephen R. Pennington, Young Ki Paik, Christopher M. Overall, Fernando J. Corrales, Ileana M. Cristea, Jennifer E. Van Eyk, Mathias Uhlén, Cecilia Lindskog, Daniel W. Chan, Amos Bairoch, James C. Waddington, Joshua L. Justice, Joshua LaBaer, Henry Rodriguez, Fuchu HeMarkus Kostrzewa, Peipei Ping, Rebekah L. Gundry, Peter Stewart, Sanjeeva Srivastava, Sudhir Srivastava, Fabio C.S. Nogueira, Gilberto B. Domont, Yves Vandenbrouck, Maggie P.Y. Lam, Sara Wennersten, Juan Antonio Vizcaino, Marc Wilkins, Jochen M. Schwenk, Emma Lundberg, Nuno Bandeira, Gyorgy Marko-Varga, Susan T. Weintraub, Charles Pineau, Ulrike Kusebauch, Robert L. Moritz, Seong Beom Ahn, Magnus Palmblad, Michael P. Snyder, Ruedi Aebersold, Mark S. Baker

Research output: Contribution to journal › Review article › peer-review

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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.

Original language	English (US)
Article number	5301
Journal	Nature communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-19045-9
State	Published - Dec 1 2020

All Science Journal Classification (ASJC) codes

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
General
Physics and Astronomy(all)

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10.1038/s41467-020-19045-9

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Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y. K., Overall, C. M., Corrales, F. J., Cristea, I. M., Van Eyk, J. E., Uhlén, M., Lindskog, C., Chan, D. W., Bairoch, A., Waddington, J. C., Justice, J. L., LaBaer, J., Rodriguez, H., ... Baker, M. S. (2020). A high-stringency blueprint of the human proteome. Nature communications, 11(1), [5301]. https://doi.org/10.1038/s41467-020-19045-9

@article{f9fcaeccde764d7592ca30a17a24d627,

title = "A high-stringency blueprint of the human proteome",

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{\textquoteright}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.",

author = "Subash Adhikari and Nice, {Edouard C.} and Deutsch, {Eric W.} and Lydie Lane and Omenn, {Gilbert S.} and Pennington, {Stephen R.} and Paik, {Young Ki} and Overall, {Christopher M.} and Corrales, {Fernando J.} and Cristea, {Ileana M.} and {Van Eyk}, {Jennifer E.} and Mathias Uhl{\'e}n and Cecilia Lindskog and Chan, {Daniel W.} and Amos Bairoch and Waddington, {James C.} and Justice, {Joshua L.} and Joshua LaBaer and Henry Rodriguez and Fuchu He and Markus Kostrzewa and Peipei Ping and Gundry, {Rebekah L.} and Peter Stewart and Sanjeeva Srivastava and Sudhir Srivastava and Nogueira, {Fabio C.S.} and Domont, {Gilberto B.} and Yves Vandenbrouck and Lam, {Maggie P.Y.} and Sara Wennersten and Vizcaino, {Juan Antonio} and Marc Wilkins and Schwenk, {Jochen M.} and Emma Lundberg and Nuno Bandeira and Gyorgy Marko-Varga and Weintraub, {Susan T.} and Charles Pineau and Ulrike Kusebauch and Moritz, {Robert L.} and Ahn, {Seong Beom} and Magnus Palmblad and Snyder, {Michael P.} and Ruedi Aebersold and Baker, {Mark S.}",

note = "Funding Information: HUPO acknowledges collaborators, proteomic scientists, independent partners, industry vendors and members of the scientific community who have contributed to the HPP. A full alphabetical listing of the Human Proteome Project members appears in the Supplementary Information. In recognition of the many accomplishments, HUPO has produced a publicly available HPP timeline available through https://hupo.org/ Proteomics-Timeline to be released with this HPP Blueprint. Parts of this work were supported by grants to ProteoRed PRB3-ISCIII, PT17/0019/0001 Comunidad de Madrid Grant B2017/BMD-3817 (F.J.C.); Korean Ministry of Health and Welfare HI13C2098 and HI16C0257 (Y.K.P.); NIH grants P30ES017885 and U24CA210967 (G.S.O.), 5U01HL-13104204, PADOM-SPO11347 and PARYB-SPO112285 (M.P.S.); NCI CPTAC U24CA210985 and NCI EDRN U24CA115102 (D.W.C.); NIH National Institute of General Medical Sciences R01GM087221 (E.W.D./R.L.M.) and R24GM127667 (E.W.D.); NIH National Institute on Aging U19AG023122 (R.L.M.); NSF DBI-1933311 (E.W.D.); CIHR COVID-19 Rapid Research Funding (F20-01013), CIHR Foundation Grant FDN:14840 and Canada Research Chair (C.M.O.); Investissement d{\textquoteright}Avenir Infrastructures Nationales en Biologie et Sant{\'e} ANR-10-INBS-08 (Proteomics French Infrastructure ProFI (Y.V.); Wellcome Trust WT101477MA and 208391/Z/17/Z (J.A.V.); Knut and Alice Wallenberg Foundation (M.U., C.L., J.M.S., E.L.); Brazilian CAPES 88887.130697, CNPq 440613/2016-7, FAPERJ E-26/210.173/2018 (G.B.D.) and FAPERJ E-26/202.650/2018 (F.C.S.N.), Australian Commonwealth NCRIS (M.S.B.); NHMRC 1010303 (M.S.B., E.C.N.); Cancer Council NSW RG19-04 (M.S.B., S.B.A., E.C.N.); Cancer Institute NSW Fellowship 15/ECF/1-38 (S.B.A.), Sydney Vital CINSW Translational Cancer Research Centre grant (M.S.B., S.B.A., S.A.), {\textquoteleft}Fight on the Beaches{\textquoteright} (M.S.B., S.B.A., E.C.N., S.A.) funding and an International Macquarie Research Excellence Scholarship (S.A.). M.S.B. thanks the Faculty of Medicine, Stanford University for a sabbatical visiting professorship. Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

month = dec,

day = "1",

doi = "10.1038/s41467-020-19045-9",

language = "English (US)",

volume = "11",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

}

Adhikari, S, Nice, EC, Deutsch, EW, Lane, L, Omenn, GS, Pennington, SR, Paik, YK, Overall, CM, Corrales, FJ, Cristea, IM, Van Eyk, JE, Uhlén, M, Lindskog, C, Chan, DW, Bairoch, A, Waddington, JC, Justice, JL, LaBaer, J, Rodriguez, H, He, F, Kostrzewa, M, Ping, P, Gundry, RL, Stewart, P, Srivastava, S, Srivastava, S, Nogueira, FCS, Domont, GB, Vandenbrouck, Y, Lam, MPY, Wennersten, S, Vizcaino, JA, Wilkins, M, Schwenk, JM, Lundberg, E, Bandeira, N, Marko-Varga, G, Weintraub, ST, Pineau, C, Kusebauch, U, Moritz, RL, Ahn, SB, Palmblad, M, Snyder, MP, Aebersold, R & Baker, MS 2020, 'A high-stringency blueprint of the human proteome', Nature communications, vol. 11, no. 1, 5301. https://doi.org/10.1038/s41467-020-19045-9

TY - JOUR

T1 - A high-stringency blueprint of the human proteome

AU - Adhikari, Subash

AU - Nice, Edouard C.

AU - Deutsch, Eric W.

AU - Lane, Lydie

AU - Omenn, Gilbert S.

AU - Pennington, Stephen R.

AU - Paik, Young Ki

AU - Overall, Christopher M.

AU - Corrales, Fernando J.

AU - Cristea, Ileana M.

AU - Van Eyk, Jennifer E.

AU - Uhlén, Mathias

AU - Lindskog, Cecilia

AU - Chan, Daniel W.

AU - Bairoch, Amos

AU - Waddington, James C.

AU - Justice, Joshua L.

AU - LaBaer, Joshua

AU - Rodriguez, Henry

AU - He, Fuchu

AU - Kostrzewa, Markus

AU - Ping, Peipei

AU - Gundry, Rebekah L.

AU - Stewart, Peter

AU - Srivastava, Sanjeeva

AU - Srivastava, Sudhir

AU - Nogueira, Fabio C.S.

AU - Domont, Gilberto B.

AU - Vandenbrouck, Yves

AU - Lam, Maggie P.Y.

AU - Wennersten, Sara

AU - Vizcaino, Juan Antonio

AU - Wilkins, Marc

AU - Schwenk, Jochen M.

AU - Lundberg, Emma

AU - Bandeira, Nuno

AU - Marko-Varga, Gyorgy

AU - Weintraub, Susan T.

AU - Pineau, Charles

AU - Kusebauch, Ulrike

AU - Moritz, Robert L.

AU - Ahn, Seong Beom

AU - Palmblad, Magnus

AU - Snyder, Michael P.

AU - Aebersold, Ruedi

AU - Baker, Mark S.

N1 - Funding Information: HUPO acknowledges collaborators, proteomic scientists, independent partners, industry vendors and members of the scientific community who have contributed to the HPP. A full alphabetical listing of the Human Proteome Project members appears in the Supplementary Information. In recognition of the many accomplishments, HUPO has produced a publicly available HPP timeline available through https://hupo.org/ Proteomics-Timeline to be released with this HPP Blueprint. Parts of this work were supported by grants to ProteoRed PRB3-ISCIII, PT17/0019/0001 Comunidad de Madrid Grant B2017/BMD-3817 (F.J.C.); Korean Ministry of Health and Welfare HI13C2098 and HI16C0257 (Y.K.P.); NIH grants P30ES017885 and U24CA210967 (G.S.O.), 5U01HL-13104204, PADOM-SPO11347 and PARYB-SPO112285 (M.P.S.); NCI CPTAC U24CA210985 and NCI EDRN U24CA115102 (D.W.C.); NIH National Institute of General Medical Sciences R01GM087221 (E.W.D./R.L.M.) and R24GM127667 (E.W.D.); NIH National Institute on Aging U19AG023122 (R.L.M.); NSF DBI-1933311 (E.W.D.); CIHR COVID-19 Rapid Research Funding (F20-01013), CIHR Foundation Grant FDN:14840 and Canada Research Chair (C.M.O.); Investissement d’Avenir Infrastructures Nationales en Biologie et Santé ANR-10-INBS-08 (Proteomics French Infrastructure ProFI (Y.V.); Wellcome Trust WT101477MA and 208391/Z/17/Z (J.A.V.); Knut and Alice Wallenberg Foundation (M.U., C.L., J.M.S., E.L.); Brazilian CAPES 88887.130697, CNPq 440613/2016-7, FAPERJ E-26/210.173/2018 (G.B.D.) and FAPERJ E-26/202.650/2018 (F.C.S.N.), Australian Commonwealth NCRIS (M.S.B.); NHMRC 1010303 (M.S.B., E.C.N.); Cancer Council NSW RG19-04 (M.S.B., S.B.A., E.C.N.); Cancer Institute NSW Fellowship 15/ECF/1-38 (S.B.A.), Sydney Vital CINSW Translational Cancer Research Centre grant (M.S.B., S.B.A., S.A.), ‘Fight on the Beaches’ (M.S.B., S.B.A., E.C.N., S.A.) funding and an International Macquarie Research Excellence Scholarship (S.A.). M.S.B. thanks the Faculty of Medicine, Stanford University for a sabbatical visiting professorship. Publisher Copyright: © 2020, The Author(s).

PY - 2020/12/1

Y1 - 2020/12/1

N2 - 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.

AB - 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.

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UR - http://www.scopus.com/inward/citedby.url?scp=85092744472&partnerID=8YFLogxK

U2 - 10.1038/s41467-020-19045-9

DO - 10.1038/s41467-020-19045-9

M3 - Review article

C2 - 33067450

AN - SCOPUS:85092744472

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 5301

ER -

A high-stringency blueprint of the human proteome

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