Metrics for the human proteome project 2013-2014 and strategies for finding missing proteins

Journal of Proteome Research

Volumn 13, Issue 1, 2014, Pages 15-20

  Lane, Lydie ^a   Bairoch, Amos ^a   Beavis, Ronald C ^b   Deutsch, Eric W ^c   Gaudet, Pascale ^a   Lundberg, Emma ^d   Omenn, Gilbert S ^c,e  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^d ALBANOVA UNIVERSITY CENTER   (Sweden)

^e UNIVERSITY OF MICHIGAN   (United States)

Author keywords

GPMdb; human protein atlas; human proteome project; metrics; missing proteins; neXtProt; PeptideAtlas

Indexed keywords

PROTEIN; PROTEOME;

ARTICLE; CHROMOSOME; HUMAN; HUMAN PROTEOME PROJECT; LEADERSHIP; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEOMICS;

CHROMOSOMES, HUMAN; HUMANS; MASS SPECTROMETRY; PROTEOME;

EID: 84891818310     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr401144x     Document Type: Article

References (25)

1. Marko-Varga, G.; Omenn, G. S.; Paik, Y. K.; Hancock, W. S. A first step toward completion of a genome-wide characterization of the human proteome J. Proteome Res. 2013, 12 (1) 1-5
2. Aebersold, R.; Bader, G. D.; Edwards, A. M.; van Eyk, J. E.; Kussmann, M.; Qin, J.; Omenn, G. S. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community J. Proteome Res. 2013, 12 (1) 23-7
3. Hood, L. E.; Omenn, G. S.; Moritz, R. L.; Aebersold, R.; Yamamoto, K. R.; Amos, M.; Hunter-Cevera, J.; Locascio, L. New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences Proteomics 2012, 12 (18) 2773-83
4. Farrah, T.; Deutsch, E. W.; Hoopmann, M. R.; Hallows, J. L.; Sun, Z.; Huang, C. Y.; Moritz, R. L. The State of the Human Proteome in 2012 as viewed through PeptideAtlas J. Proteome Res. 2013, 12 (1) 162-71
5. Gaudet, P.; Argoud-Puy, G.; Cusin, I.; Duek, P.; Evalet, O.; Gateau, A.; Gleizes, A.; Pereira, M.; Zahn-Zabal, M.; Zwahlen, C.; Bairoch, A.; Lane, L. neXtProt: organizing protein knowledge in the context of human proteome projects J. Proteome Res. 2013, 12 (1) 293-8
6. Goode, R. J.; Yu, S.; Kannan, A.; Christiansen, J. H.; Beitz, A.; Hancock, W. S.; Nice, E.; Smith, A. I. The proteome browser web portal J. Proteome Res. 2013, 12 (1) 172-8
7. Guo, F.; Wang, D.; Liu, Z.; Lu, L.; Zhang, W.; Sun, H.; Zhang, H.; Ma, J.; Wu, S.; Li, N.; Jiang, Y.; Zhu, W.; Qin, J.; Xu, P.; Li, D.; He, F. CAPER: a chromosome-assembled human proteome browsER J. Proteome Res. 2013, 12 (1) 179-86
8. Jeong, S. K.; Lee, H. J.; Na, K.; Cho, J. Y.; Lee, M. J.; Kwon, J. Y.; Kim, H.; Park, Y. M.; Yoo, J. S.; Hancock, W. S.; Paik, Y. K. GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes J. Proteome Res. 2013, 12 (1) 106-11
9. Zgoda, V. G.; Kopylov, A. T.; Tikhonova, O. V.; Moisa, A. A.; Pyndyk, N. V.; Farafonova, T. E.; Novikova, S. E.; Lisitsa, A. V.; Ponomarenko, E. A.; Poverennaya, E. V.; Radko, S. P.; Khmeleva, S. A.; Kurbatov, L. K.; Filimonov, A. D.; Bogolyubova, N. A.; Ilgisonis, E. V.; Chernobrovkin, A. L.; Ivanov, A. S.; Medvedev, A. E.; Mezentsev, Y. V.; Moshkovskii, S. A.; Naryzhny, S. N.; Ilina, E. N.; Kostrjukova, E. S.; Alexeev, D. G.; Tyakht, A. V.; Govorun, V. M.; Archakov, A. I. Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells J. Proteome Res. 2013, 12 (1) 123-34
10. Martins-de-Souza, D.; Carvalho, P.; Schmitt, A.; Junqueira, M.; Nogueira, F.; Turck, C.; Domont, G. Deciphering the human brain proteome as part of the chromosome 15-centric human proteome project J. Proteome Res. 2013, 10.1021/pr4009157
11. Beck, M.; Schmidt, A.; Malmstroem, J.; Claassen, M.; Ori, A.; Szymborska, A.; Herzog, F.; Rinner, O.; Ellenberg, J.; Aebersold, R. The quantitative proteome of a human cell line Mol. Syst. Biol. 2011, 7, 549
12. Nagaraj, N.; Wisniewski, J. R.; Geiger, T.; Cox, J.; Kircher, M.; Kelso, J.; Paabo, S.; Mann, M. Deep proteome and transcriptome mapping of a human cancer cell line Mol. Syst. Biol. 2011, 7, 548
13. Geiger, T.; Wehner, A.; Schaab, C.; Cox, J.; Mann, M. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins Mol. Cell. Proteomics 2012, 11 (3) M111 014050
14. Neuhauser, N.; Nagaraj, N.; McHardy, P.; Zanivan, S.; Scheltema, R.; Cox, J.; Mann, M. 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
15. Fagerberg, L.; Oksvold, P.; Skogs, M.; Algenas, C.; Lundberg, E.; Ponten, F.; Sivertsson, A.; Odeberg, J.; Klevebring, D.; Kampf, C.; Asplund, A.; Sjostedt, E.; Al-Khalili Szigyarto, C.; Edqvist, P. H.; Olsson, I.; Rydberg, U.; Hudson, P.; Ottosson Takanen, J.; Berling, H.; Bjorling, L.; Tegel, H.; Rockberg, J.; Nilsson, P.; Navani, S.; Jirstrom, K.; Mulder, J.; Schwenk, J. M.; Zwahlen, M.; Hober, S.; Forsberg, M.; von Feilitzen, K.; Uhlen, M. Contribution of antibody-based protein profiling to the Human Chromosome-centric Proteome Project (C-HPP) J. Proteome Res. 2013, 12 (6) 2439-48
16. Lee, H. J.; Jeong, S. K.; Na, K.; Lee, M. J.; Lee, S. H.; Lim, J. S.; Cha, H. J.; Cho, J. Y.; Kwon, J. Y.; Kim, H.; Song, S. Y.; Yoo, J. S.; Park, Y. M.; Hancock, W. S.; Paik, Y. K. Comprehensive genome-wide proteomic analysis of human placental tissue for the chromosome-centric human proteome project J. Proteome Res. 2013, 12 (6) 2458-66
17. Zhong, J.; Cui, Y.; Guo, J.; Chen, Z.; Yang, L.; He, Q.; Wang, T. Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration. J. Proteome Res. 2013, 10.1021/pr4007409.
18. Danielsson, F.; Wiking, M.; Mahdessian, D.; Skogs, M.; Ait Blal, H.; Hjelmare, M.; Stadler, C.; Uhlen, M.; Lundberg, E. RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins J. Proteome Res. 2013, 12 (1) 299-307
19. Liu, S.; Im, H.; Bairoch, A.; Cristofanilli, M.; Chen, R.; Deutsch, E. W.; Dalton, S.; Fenyo, D.; Fanayan, S.; Gates, C.; Gaudet, P.; Hincapie, M.; Hanash, S.; Kim, H.; Jeong, S. K.; Lundberg, E.; Mias, G.; Menon, R.; Mu, Z.; Nice, E.; Paik, Y. K.; Uhlen, M.; Wells, L.; Wu, S. L.; Yan, F.; Zhang, F.; Zhang, Y.; Snyder, M.; Omenn, G. S.; Beavis, R. C.; Hancock, W. S. A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17 J Proteome Res 2013, 12 (1) 45-57
20. Risk, B. A.; Spitzer, W. J.; Giddings, M. C. Peppy: proteogenomic search software J. Proteome Res. 2013, 12 (6) 3019-25
21. Munoz, J.; Low, T. Y.; Kok, Y. J.; Chin, A.; Frese, C. K.; Ding, V.; Choo, A.; Heck, A. J. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells Mol. Syst. Biol. 2011, 7, 550
22. Muraoka, S.; Kume, H.; Adachi, J.; Shiromizu, T.; Watanabe, S.; Masuda, T.; Ishihama, Y.; Tomonaga, T. In-depth membrane proteomic study of breast cancer tissues for the generation of a chromosome-based protein list J Proteome Res. 2013, 12 (1) 208-13
23. Punta, M.; Coggill, P. C.; Eberhardt, R. Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K.; Ceric, G.; Clements, J.; Heger, A.; Holm, L.; Sonnhammer, E. L.; Eddy, S. R.; Bateman, A.; Finn, R. D. The Pfam protein families database Nucleic Acids Res. 2012, 40 (Database issue) D290-301
24. Andreeva, A.; Howorth, D.; Chandonia, J. M.; Brenner, S. E.; Hubbard, T. J.; Chothia, C.; Murzin, A. G. Data growth and its impact on the SCOP database: new developments Nucleic Acids Res. 2008, 36 (Database issue) D419-25
25. Tang, H. Y.; Ali-Khan, N.; Echan, L. A.; Levenkova, N.; Rux, J. J.; Speicher, D. W. 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