Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

Gilbert S. Omenn; Lydie Lane; Christopher M. Overall; Young Ki Paik; Ileana M. Cristea; Fernando J. Corrales; Cecilia Lindskog; Susan Weintraub; Michael H.A. Roehrl; Siqi Liu; Nuno Bandeira; Sudhir Srivastava; Yu Ju Chen; Ruedi Aebersold; Robert L. Moritz; Eric W. Deutsch

doi:10.1021/acs.jproteome.1c00590

Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

Gilbert S. Omenn
, Lydie Lane
, Christopher M. Overall
, Young Ki Paik
, Ileana M. Cristea
, Fernando J. Corrales
, Cecilia Lindskog
, Susan Weintraub
, Michael H.A. Roehrl
, Siqi Liu
, Nuno Bandeira
, Sudhir Srivastava
, Yu Ju Chen
, Ruedi Aebersold
, Robert L. Moritz
, Eric W. Deutsch

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

33 Scopus citations

Abstract

The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 »357 (92.8%) of the 19 »778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.

Original language	English (US)
Pages (from-to)	5227-5240
Number of pages	14
Journal	Journal of Proteome Research
Volume	20
Issue number	12
DOIs	https://doi.org/10.1021/acs.jproteome.1c00590
State	Published - Dec 3 2021

All Science Journal Classification (ASJC) codes

Biochemistry
General Chemistry

Keywords

Biology and Disease-HPP (B/D-HPP)
Chromosome-centric HPP (C-HPP)
Human Protein Atlas
Human Proteome Project (HPP)
Mass Spectrometry Interactive Virtual Environment (MassIVE)
PeptideAtlas
missing proteins (MP)
neXtProt protein existence (PE) metrics
non-MS PE1 proteins
uncharacterized protein existence 1 (uPE1)

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10.1021/acs.jproteome.1c00590

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Omenn, G. S., Lane, L., Overall, C. M., Paik, Y. K., Cristea, I. M., Corrales, F. J., Lindskog, C., Weintraub, S., Roehrl, M. H. A., Liu, S., Bandeira, N., Srivastava, S., Chen, Y. J., Aebersold, R., Moritz, R. L., & Deutsch, E. W. (2021). Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. Journal of Proteome Research, 20(12), 5227-5240. https://doi.org/10.1021/acs.jproteome.1c00590

@article{47ddb52b06834948ac13bac54c468807,

title = "Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project",

abstract = "The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 »357 (92.8\%) of the 19 »778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.",

keywords = "Biology and Disease-HPP (B/D-HPP), Chromosome-centric HPP (C-HPP), Human Protein Atlas, Human Proteome Project (HPP), Mass Spectrometry Interactive Virtual Environment (MassIVE), PeptideAtlas, missing proteins (MP), neXtProt protein existence (PE) metrics, non-MS PE1 proteins, uncharacterized protein existence 1 (uPE1)",

author = "Omenn, \{Gilbert S.\} and Lydie Lane and Overall, \{Christopher M.\} and Paik, \{Young Ki\} and Cristea, \{Ileana M.\} and Corrales, \{Fernando J.\} and Cecilia Lindskog and Susan Weintraub and Roehrl, \{Michael H.A.\} and Siqi Liu and Nuno Bandeira and Sudhir Srivastava and Chen, \{Yu Ju\} and Ruedi Aebersold and Moritz, \{Robert L.\} and Deutsch, \{Eric W.\}",

note = "Publisher Copyright: {\textcopyright} 2021 American Chemical Society.",

year = "2021",

month = dec,

day = "3",

doi = "10.1021/acs.jproteome.1c00590",

language = "English (US)",

volume = "20",

pages = "5227--5240",

journal = "Journal of Proteome Research",

issn = "1535-3893",

publisher = "American Chemical Society",

number = "12",

}

Omenn, GS, Lane, L, Overall, CM, Paik, YK, Cristea, IM, Corrales, FJ, Lindskog, C, Weintraub, S, Roehrl, MHA, Liu, S, Bandeira, N, Srivastava, S, Chen, YJ, Aebersold, R, Moritz, RL & Deutsch, EW 2021, 'Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project', Journal of Proteome Research, vol. 20, no. 12, pp. 5227-5240. https://doi.org/10.1021/acs.jproteome.1c00590

TY - JOUR

T1 - Progress Identifying and Analyzing the Human Proteome

T2 - 2021 Metrics from the HUPO Human Proteome Project

AU - Omenn, Gilbert S.

AU - Lane, Lydie

AU - Overall, Christopher M.

AU - Paik, Young Ki

AU - Cristea, Ileana M.

AU - Corrales, Fernando J.

AU - Lindskog, Cecilia

AU - Weintraub, Susan

AU - Roehrl, Michael H.A.

AU - Liu, Siqi

AU - Bandeira, Nuno

AU - Srivastava, Sudhir

AU - Chen, Yu Ju

AU - Aebersold, Ruedi

AU - Moritz, Robert L.

AU - Deutsch, Eric W.

PY - 2021/12/3

Y1 - 2021/12/3

N2 - The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 »357 (92.8%) of the 19 »778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.

AB - The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 »357 (92.8%) of the 19 »778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.

KW - Biology and Disease-HPP (B/D-HPP)

KW - Chromosome-centric HPP (C-HPP)

KW - Human Protein Atlas

KW - Human Proteome Project (HPP)

KW - Mass Spectrometry Interactive Virtual Environment (MassIVE)

KW - PeptideAtlas

KW - missing proteins (MP)

KW - neXtProt protein existence (PE) metrics

KW - non-MS PE1 proteins

KW - uncharacterized protein existence 1 (uPE1)

UR - https://www.scopus.com/pages/publications/85118767127

UR - https://www.scopus.com/pages/publications/85118767127#tab=citedBy

U2 - 10.1021/acs.jproteome.1c00590

DO - 10.1021/acs.jproteome.1c00590

M3 - Review article

C2 - 34670092

AN - SCOPUS:85118767127

SN - 1535-3893

VL - 20

SP - 5227

EP - 5240

JO - Journal of Proteome Research

JF - Journal of Proteome Research

IS - 12

ER -

Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

Abstract

All Science Journal Classification (ASJC) codes

Keywords

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