Metrics for the human proteome project 2015: Progress on the human proteome and guidelines for high-confidence protein identification

Journal of Proteome Research

Volumn 14, Issue 9, 2015, Pages 3452-3460

  Omenn, Gilbert S ^a   Lane, Lydie ^b   Lundberg, Emma K ^c   Beavis, Ronald C ^d   Nesvizhskii, Alexey I ^e   Deutsch, Eric W ^f  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c SCIENCE FOR LIFE LABORATORY   (Sweden)

^d UNIVERSITY OF MANITOBA   (Canada)

^e UNIVERSITY OF MICHIGAN   (United States)

^f INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

Global Proteome Machine database (GPMDB); guidelines; high confidence protein identifications; HPP metrics; Human Protein Atlas; Human Proteome Project; missing proteins; neXtProt; novel proteins; PeptideAtlas

Indexed keywords

PROTEIN; PROTEOME;

AMINO ACID SEQUENCE; ARTICLE; CANCER CELL LINE; CELLULAR DISTRIBUTION; CHROMOSOME 12; CHROMOSOME 22; GENE EXPRESSION; GENOMICS; HUMAN; IMMUNOHISTOCHEMISTRY; MASS SPECTROMETRY; NONHUMAN; OLFACTORY RECEPTOR; OVARY CANCER; PRACTICE GUIDELINE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; PSEUDOGENE; Y CHROMOSOME; CHEMISTRY;

GUIDELINES AS TOPIC; HUMANS; PROTEINS; PROTEOME;

EID: 84941057782     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00499     Document Type: Article

References (40)

1. Legrain, P.; Aebersold, R.; Archakov, A.; Bairoch, A.; Bala, K.; Beretta, L.; Bergeron, J.; Borchers, C. H.; Corthals, G. L.; Costello, C. E.; Deutsch, E. W.; Domon, B.; Hancock, W.; He, F.; Hochstrasser, D.; Marko-Varga, G.; Salekdeh, G. H.; Sechi, S.; Snyder, M.; Srivastava, S.; Uhlen, M.; Wu, C. H.; Yamamoto, T.; Paik, Y. K.; Omenn, G. S. The human proteome project: current state and future direction Mol. Cell. Proteomics 2011, 10 (7) M111.009993 10.1074/mcp.M111.009993
2. 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 10.1021/pr300830v
3. 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 10.1021/pr301183a
4. Lane, L.; Bairoch, A.; Beavis, R. C.; Deutsch, E. W.; Gaudet, P.; Lundberg, E.; Omenn, G. S. Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins J. Proteome Res. 2014, 13 (1) 15-20 10.1021/pr401144x
5. Gaudet, P.; Michel, P. A.; Zahn-Zabal, M.; Cusin, I.; Duek, P. D.; Evalet, O.; Gateau, A.; Gleizes, A.; Pereira, M.; Teixeira, D.; Zhang, Y.; Lane, L.; Bairoch, A. The neXtProt knowledgebase on human proteins: current status Nucleic Acids Res. 2015, 43 (D1) D764-70 10.1093/nar/gku1178
6. Fenyo, D.; Beavis, R. C. The GPMDB REST interface Bioinformatics 2015, 31, 2056 10.1093/bioinformatics/btv107
7. Uhlen, M.; Fagerberg, L.; Hallstrom, B. M.; Lindskog, C.; Oksvold, P.; Mardinoglu, A.; Sivertsson, A.; Kampf, C.; Sjostedt, E.; Asplund, A.; Olsson, I.; Edlund, K.; Lundberg, E.; Navani, S.; Szigyarto, C. A.; Odeberg, J.; Djureinovic, D.; Takanen, J. O.; Hober, S.; Alm, T.; Edqvist, P. H.; Berling, H.; Tegel, H.; Mulder, J.; Rockberg, J.; Nilsson, P.; Schwenk, J. M.; Hamsten, M.; von Feilitzen, K.; Forsberg, M.; Persson, L.; Johansson, F.; Zwahlen, M.; von Heijne, G.; Nielsen, J.; Ponten, F. Proteomics. Tissue-based map of the human proteome Science 2015, 347 (6220) 1260419 10.1126/science.1260419
8. Deutsch, E. W.; Sun, Z.; Campbell, D.; Kusebauch, U.; Chu, C. S.; Mendoza, L.; Shteynberg, D.; Omenn, G. S.; Moritz, R. L. The state of the Human Proteome in 2015 as viewed through PeptideAtlas: enhacing accuracy and coverage J. Proteome Res. 2015, 10.1021/acs.jproteome.5b00500
9. The UniProt Consortium Activities at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2014, 42 (Database issue) D191-8 10.1093/nar/gkt1140
10. Vizcaino, J. A.; Deutsch, E. W.; Wang, R.; Csordas, A.; Reisinger, F.; Rios, D.; Dianes, J. A.; Sun, Z.; Farrah, T.; Bandeira, N.; Binz, P. A.; Xenarios, I.; Eisenacher, M.; Mayer, G.; Gatto, L.; Campos, A.; Chalkley, R. J.; Kraus, H. J.; Albar, J. P.; Martinez-Bartolome, S.; Apweiler, R.; Omenn, G. S.; Martens, L.; Jones, A. R.; Hermjakob, H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination Nat. Biotechnol. 2014, 32 (3) 223-6 10.1038/nbt.2839
11. Guo, X.; Trudgian, D. C.; Lemoff, A.; Yadavalli, S.; Mirzaei, H. Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics Mol. Cell. Proteomics 2014, 13 (6) 1573-84 10.1074/mcp.M113.035170
12. Kim, M. S.; Pinto, S. M.; Getnet, D.; Nirujogi, R. S.; Manda, S. S.; Chaerkady, R.; Madugundu, A. K.; Kelkar, D. S.; Isserlin, R.; Jain, S.; Thomas, J. K.; Muthusamy, B.; Leal-Rojas, P.; Kumar, P.; Sahasrabuddhe, N. A.; Balakrishnan, L.; Advani, J.; George, B.; Renuse, S.; Selvan, L. D.; Patil, A. H.; Nanjappa, V.; Radhakrishnan, A.; Prasad, S.; Subbannayya, T.; Raju, R.; Kumar, M.; Sreenivasamurthy, S. K.; Marimuthu, A.; Sathe, G. J.; Chavan, S.; Datta, K. K.; Subbannayya, Y.; Sahu, A.; Yelamanchi, S. D.; Jayaram, S.; Rajagopalan, P.; Sharma, J.; Murthy, K. R.; Syed, N.; Goel, R.; Khan, A. A.; Ahmad, S.; Dey, G.; Mudgal, K.; Chatterjee, A.; Huang, T. C.; Zhong, J.; Wu, X.; Shaw, P. G.; Freed, D.; Zahari, M. S.; Mukherjee, K. K.; Shankar, S.; Mahadevan, A.; Lam, H.; Mitchell, C. J.; Shankar, S. K.; Satishchandra, P.; Schroeder, J. T.; Sirdeshmukh, R.; Maitra, A.; Leach, S. D.; Drake, C. G.; Halushka, M. K.; Prasad, T. S.; Hruban, R. H.; Kerr, C. L.; Bader, G. D.; Iacobuzio-Donahue, C. A.; Gowda, H.; Pandey, A. A draft map of the human proteome Nature 2014, 509 (7502) 575-81 10.1038/nature13302
13. Wilhelm, M.; Schlegl, J.; Hahne, H.; Gholami, A. M.; Lieberenz, M.; Savitski, M. M.; Ziegler, E.; Butzmann, L.; Gessulat, S.; Marx, H.; Mathieson, T.; Lemeer, S.; Schnatbaum, K.; Reimer, U.; Wenschuh, H.; Mollenhauer, M.; Slotta-Huspenina, J.; Boese, J. H.; Bantscheff, M.; Gerstmair, A.; Faerber, F.; Kuster, B. Mass-spectrometry-based draft of the human proteome Nature 2014, 509 (7502) 582-7 10.1038/nature13319
14. Zhang, B.; Wang, J.; Wang, X.; Zhu, J.; Liu, Q.; Shi, Z.; Chambers, M. C.; Zimmerman, L. J.; Shaddox, K. F.; Kim, S.; Davies, S. R.; Wang, S.; Wang, P.; Kinsinger, C. R.; Rivers, R. C.; Rodriguez, H.; Townsend, R. R.; Ellis, M. J.; Carr, S. A.; Tabb, D. L.; Coffey, R. J.; Slebos, R. J.; Liebler, D. C. Proteogenomic characterization of human colon and rectal cancer Nature 2014, 513 (7518) 382-7 10.1038/nature13438
15. Pinto, S. M.; Manda, S. S.; Kim, M. S.; Taylor, K.; Selvan, L. D.; Balakrishnan, L.; Subbannayya, T.; Yan, F.; Prasad, T. S.; Gowda, H.; Lee, C.; Hancock, W. S.; Pandey, A. Functional annotation of proteome encoded by human chromosome 22 J. Proteome Res. 2014, 13 (6) 2749-60 10.1021/pr401169d
16. Manda, S. S.; Nirujogi, R. S.; Pinto, S. M.; Kim, M. S.; Datta, K. K.; Sirdeshmukh, R.; Prasad, T. S.; Thongboonkerd, V.; Pandey, A.; Gowda, H. Identification and characterization of proteins encoded by chromosome 12 as part of chromosome-centric human proteome project J. Proteome Res. 2014, 13 (7) 3166-77 10.1021/pr401123v
17. Savitski, M. M.; Wilhelm, M.; Hahne, H.; Kuster, B.; Bantscheff, M. A scalable approach for protein false discovery rate estimation in large proteomic data sets Mol. Cell. Proteomics 2015, M114, 046995 10.1074/mcp.M114.046995
18. Sjostedt, E.; Fagerberg, L.; Hallstrom, B. M.; Haggmark, A.; Mitsios, N.; Nilsson, P.; Ponten, F.; Hokfelt, T.; Uhlen, M.; Mulder, J. Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex PLoS One 2015, 10 (6) e0130028 10.1371/journal.pone.0130028
19. Kampf, C.; Mardinoglu, A.; Fagerberg, L.; Hallstrom, B. M.; Edlund, K.; Lundberg, E.; Ponten, F.; Nielsen, J.; Uhlen, M. The human liver-specific proteome defined by transcriptomics and antibody-based profiling FASEB J. 2014, 28 (7) 2901-14 10.1096/fj.14-250555
20. Djureinovic, D.; Fagerberg, L.; Hallstrom, B.; Danielsson, A.; Lindskog, C.; Uhlen, M.; Ponten, F. The human testis-specific proteome defined by transcriptomics and antibody-based profiling Mol. Hum. Reprod. 2014, 20 (6) 476-88 10.1093/molehr/gau018
21. Habuka, M.; Fagerberg, L.; Hallstrom, B. M.; Kampf, C.; Edlund, K.; Sivertsson, A.; Yamamoto, T.; Ponten, F.; Uhlen, M.; Odeberg, J. The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling PLoS One 2014, 9 (12) e116125 10.1371/journal.pone.0116125
22. Danielsson, A.; Ponten, F.; Fagerberg, L.; Hallstrom, B. M.; Schwenk, J. M.; Uhlen, M.; Korsgren, O.; Lindskog, C. The human pancreas proteome defined by transcriptomics and antibody-based profiling PLoS One 2014, 9 (12) e115421 10.1371/journal.pone.0115421
23. Edqvist, P. H.; Fagerberg, L.; Hallstrom, B. M.; Danielsson, A.; Edlund, K.; Uhlen, M.; Ponten, F. Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling J. Histochem. Cytochem. 2015, 63 (2) 129-41 10.1369/0022155414562646
24. Mardinoglu, A.; Kampf, C.; Asplund, A.; Fagerberg, L.; Hallstrom, B. M.; Edlund, K.; Bluher, M.; Ponten, F.; Uhlen, M.; Nielsen, J. Defining the human adipose tissue proteome to reveal metabolic alterations in obesity J. Proteome Res. 2014, 13 (11) 5106-19 10.1021/pr500586e
25. Kampf, C.; Mardinoglu, A.; Fagerberg, L.; Hallstrom, B. M.; Danielsson, A.; Nielsen, J.; Ponten, F.; Uhlen, M. Defining the human gallbladder proteome by transcriptomics and affinity proteomics Proteomics 2014, 14 (21-22) 2498-507 10.1002/pmic.201400201
26. Lindskog, C.; Fagerberg, L.; Hallstrom, B.; Edlund, K.; Hellwig, B.; Rahnenfuhrer, J.; Kampf, C.; Uhlen, M.; Ponten, F.; Micke, P. The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling FASEB J. 2014, 28 (12) 5184-96 10.1096/fj.14-254862
27. Gremel, G.; Wanders, A.; Cedernaes, J.; Fagerberg, L.; Hallstrom, B.; Edlund, K.; Sjostedt, E.; Uhlen, M.; Ponten, F. The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling J. Gastroenterol. 2015, 50 (1) 46-57 10.1007/s00535-014-0958-7
28. Lindskog, C.; Linne, J.; Fagerberg, L.; Hallstrom, B. M.; Sundberg, C. J.; Lindholm, M.; Huss, M.; Kampf, C.; Choi, H.; Liem, D. A.; Ping, P.; Varemo, L.; Mardinoglu, A.; Nielsen, J.; Larsson, E.; Ponten, F.; Uhlen, M. The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling BMC Genomics 2015, 16 (1) 475 10.1186/s12864-015-1686-y
29. Zeiler, M.; Straube, W. L.; Lundberg, E.; Uhlen, M.; Mann, M. A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines Mol. Cell. Proteomics 2012, 11 (3) O111.009613 10.1074/mcp.O111.009613
30. Frankish, A.; Uszczynska, B.; Ritchie, G. R.; Gonzalez, J. M.; Pervouchine, D.; Petryszak, R.; Mudge, J. M.; Fonseca, N.; Brazma, A.; Guigo, R.; Harrow, J. Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction BMC Genomics 2015, 16 (Suppl 8) S2 10.1186/1471-2164-16-S8-S2
31. Nesvizhskii, A. I. Proteogenomics: concepts, applications and computational strategies Nat. Methods 2014, 11 (11) 1114-25 10.1038/nmeth.3144
32. Ezkurdia, I.; Vazquez, J.; Valencia, A.; Tress, M. Analyzing the first drafts of the human proteome J. Proteome Res. 2014, 13, 3854 10.1021/pr500572z
33. Batruch, I.; Smith, C. R.; Mullen, B. J.; Grober, E.; Lo, K. C.; Diamandis, E. P.; Jarvi, K. A. Analysis of seminal plasma from patients with non-obstructive azoospermia and identification of candidate biomarkers of male infertility J. Proteome Res. 2012, 11 (3) 1503-11 10.1021/pr200812p
34. Xu, L. L.; Stackhouse, B. G.; Florence, K.; Zhang, W.; Shanmugam, N.; Sesterhenn, I. A.; Zou, Z.; Srikantan, V.; Augustus, M.; Roschke, V.; Carter, K.; McLeod, D. G.; Moul, J. W.; Soppett, D.; Srivastava, S. PSGR, a novel prostate-specific gene with homology to a G protein-coupled receptor, is overexpressed in prostate cancer Cancer Res. 2000, 60 (23) 6568-72
35. Reiter, L.; Claassen, M.; Schrimpf, S. P.; Jovanovic, M.; Schmidt, A.; Buhmann, J. M.; Hengartner, M. O.; Aebersold, R. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry Mol. Cell. Proteomics 2009, 8 (11) 2405-17 10.1074/mcp.M900317-MCP200
36. Perez-Riverol, Y.; Alpi, E.; Wang, R.; Hermjakob, H.; Vizcaino, J. A. Making proteomics data accessible and reusable: current state of proteomics databases and repositories Proteomics 2015, 15 (5-6) 930-950 10.1002/pmic.201400302
37. Cox, J., Controlling false discovery rates (FDRS) in genome-wide proteomics datasets, Abstract O-9, EuPA Annual Meeting, Milan, Italy, June 24, 2015.
38. Flicek, P.; Amode, M. R.; Barrell, D.; Beal, K.; Billis, K.; Brent, S.; Carvalho-Silva, D.; Clapham, P.; Coates, G.; Fitzgerald, S.; Gil, L.; Giron, C. G.; Gordon, L.; Hourlier, T.; Hunt, S.; Johnson, N.; Juettemann, T.; Kahari, A. K.; Keenan, S.; Kulesha, E.; Martin, F. J.; Maurel, T.; McLaren, W. M.; Murphy, D. N.; Nag, R.; Overduin, B.; Pignatelli, M.; Pritchard, B.; Pritchard, E.; Riat, H. S.; Ruffier, M.; Sheppard, D.; Taylor, K.; Thormann, A.; Trevanion, S. J.; Vullo, A.; Wilder, S. P.; Wilson, M.; Zadissa, A.; Aken, B. L.; Birney, E.; Cunningham, F.; Harrow, J.; Herrero, J.; Hubbard, T. J.; Kinsella, R.; Muffato, M.; Parker, A.; Spudich, G.; Yates, A.; Zerbino, D. R.; Searle, S. M. Ensembl 2014 Nucleic Acids Res. 2014, 42 (Database issue) D749-D755 10.1093/nar/gkt1196
39. Shanmugam, A. K.; Yocum, A. K.; Nesvizhskii, A. I. Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS J. Proteome Res. 2014, 13 (9) 4113-9 10.1021/pr500496p
40. Farrah, T.; Deutsch, E. W.; Omenn, G. S.; Sun, Z.; Watts, J. D.; Yamamoto, T.; Shteynberg, D.; Harris, M. M.; Moritz, R. L. State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project J. Proteome Res. 2014, 13 (1) 60-75 10.1021/pr4010037