Metrics for the Human Proteome Project 2013-2014 and Strategies for Finding Missing Proteins

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2013 Dec 25

PMID 24364385

Citations 53

Authors

Lydie Lane

Amos Bairoch

Ronald C Beavis

Eric W Deutsch

Pascale Gaudet

Emma Lundberg

Gilbert S Omenn

Affiliations

Soon will be listed here.

Abstract

One year ago the Human Proteome Project (HPP) leadership designated the baseline metrics for the Human Proteome Project to be based on neXtProt with a total of 13,664 proteins validated at protein evidence level 1 (PE1) by mass spectrometry, antibody-capture, Edman sequencing, or 3D structures. Corresponding chromosome-specific data were provided from PeptideAtlas, GPMdb, and Human Protein Atlas. This year, the neXtProt total is 15,646 and the other resources, which are inputs to neXtProt, have high-quality identifications and additional annotations for 14,012 in PeptideAtlas, 14,869 in GPMdb, and 10,976 in HPA. We propose to remove 638 genes from the denominator that are "uncertain" or "dubious" in Ensembl, UniProt/SwissProt, and neXtProt. That leaves 3844 "missing proteins", currently having no or inadequate documentation, to be found from a new denominator of 19,490 protein-coding genes. We present those tabulations and web links and discuss current strategies to find the missing proteins.

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References

Nagaraj N, Wisniewski J, Geiger T, Cox J, Kircher M, Kelso J . Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol. 2011; 7:548. PMC: 3261714. DOI: 10.1038/msb.2011.81. View

Martins-de-Souza D, Carvalho P, Schmitt A, Junqueira M, Nogueira F, Turck C . Deciphering the human brain proteome: characterization of the anterior temporal lobe and corpus callosum as part of the Chromosome 15-centric Human Proteome Project. J Proteome Res. 2013; 13(1):147-57. DOI: 10.1021/pr4009157. View

Risk B, Spitzer W, Giddings M . Peppy: proteogenomic search software. J Proteome Res. 2013; 12(6):3019-25. PMC: 4117251. DOI: 10.1021/pr400208w. View

Aebersold R, Bader G, Edwards A, Van Eyk J, Kussmann M, Qin J . The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J Proteome Res. 2012; 12(1):23-7. DOI: 10.1021/pr301151m. View

Fagerberg L, Oksvold P, Skogs M, Algenas C, Lundberg E, Ponten F . Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP). J Proteome Res. 2013; 12(6):2439-48. DOI: 10.1021/pr300924j. View

Guo F, Wang D, Liu Z, Lu L, Zhang W, Sun H . CAPER: a chromosome-assembled human proteome browsER. J Proteome Res. 2012; 12(1):179-86. DOI: 10.1021/pr300831z. View

Neuhauser N, Nagaraj N, McHardy P, Zanivan S, Scheltema R, Cox J . High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome. J Proteome Res. 2013; 12(6):2858-68. DOI: 10.1021/pr400181q. View

Goode R, Yu S, Kannan A, Christiansen J, Beitz A, Hancock W . The proteome browser web portal. J Proteome Res. 2012; 12(1):172-8. DOI: 10.1021/pr3010056. View

Munoz J, Low T, Kok Y, Chin A, Frese C, Ding V . The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol Syst Biol. 2011; 7:550. PMC: 3261715. DOI: 10.1038/msb.2011.84. View

10.

Punta M, Coggill P, Eberhardt R, Mistry J, Tate J, Boursnell C . The Pfam protein families database. Nucleic Acids Res. 2011; 40(Database issue):D290-301. PMC: 3245129. DOI: 10.1093/nar/gkr1065. View

11.

Andreeva A, Howorth D, Chandonia J, Brenner S, Hubbard T, Chothia C . Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2007; 36(Database issue):D419-25. PMC: 2238974. DOI: 10.1093/nar/gkm993. View

12.

Marko-Varga G, Omenn G, Paik Y, Hancock W . A first step toward completion of a genome-wide characterization of the human proteome. J Proteome Res. 2012; 12(1):1-5. DOI: 10.1021/pr301183a. View

13.

Tang H, Ali-Khan N, Echan L, Levenkova N, Rux J, Speicher D . A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics. 2005; 5(13):3329-42. DOI: 10.1002/pmic.200401275. View

14.

Danielsson F, Wiking M, Mahdessian D, Skogs M, Blal H, Hjelmare M . RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins. J Proteome Res. 2012; 12(1):299-307. DOI: 10.1021/pr3009308. View

15.

Farrah T, Deutsch E, Hoopmann M, Hallows J, Sun Z, Huang C . The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res. 2012; 12(1):162-71. PMC: 3928036. DOI: 10.1021/pr301012j. View

16.

Gaudet P, Argoud-Puy G, Cusin I, Duek P, Evalet O, Gateau A . neXtProt: organizing protein knowledge in the context of human proteome projects. J Proteome Res. 2012; 12(1):293-8. DOI: 10.1021/pr300830v. View

17.

Muraoka S, Kume H, Adachi J, Shiromizu T, Watanabe S, Masuda T . In-depth membrane proteomic study of breast cancer tissues for the generation of a chromosome-based protein list. J Proteome Res. 2012; 12(1):208-13. DOI: 10.1021/pr300824m. View

18.

Hood L, Omenn G, Moritz R, Aebersold R, Yamamoto K, Amos M . New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences. Proteomics. 2012; 12(18):2773-83. PMC: 4005326. DOI: 10.1002/pmic.201270086. View

19.

Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A . The quantitative proteome of a human cell line. Mol Syst Biol. 2011; 7:549. PMC: 3261713. DOI: 10.1038/msb.2011.82. View

20.

Jeong S, Lee H, Na K, Cho J, Lee M, Kwon J . GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes. J Proteome Res. 2012; 12(1):106-11. DOI: 10.1021/pr3009447. View