State of the human proteome in 2014/2015 As viewed through peptideatlas: Enhancing accuracy and coverage through the atlas prophet

Journal of Proteome Research

Volumn 14, Issue 9, 2015, Pages 3461-3473

  Deutsch, Eric W ^a   Sun, Zhi ^a   Campbell, David ^a   Kusebauch, Ulrike ^a   Chu, Caroline S ^a   Mendoza, Luis ^a   Shteynberg, David ^a   Omenn, Gilbert S ^a,b   Moritz, Robert L ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b UNIVERSITY OF MICHIGAN SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Human Proteome Project; observed proteome; PeptideAtlas; repositories; shotgun proteomics; tandem mass spectrometry

Indexed keywords

AMINO ACID; PROTEIN; PROTEIN VARIANT; PROTEOME;

AMINO ACID SEQUENCE; ARTICLE; HUMAN; INFORMATION PROCESSING; MASS SPECTROMETRY; MEASUREMENT ACCURACY; PEPTIDE ANALYSIS; PEPTIDE LIBRARY; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUALITY CONTROL; TANDEM MASS SPECTROMETRY; AMINO ACID SUBSTITUTION; CHEMISTRY; MOLECULAR GENETICS; PROTEIN DATABASE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; DATABASES, PROTEIN; HUMANS; MOLECULAR SEQUENCE DATA; PROTEINS; PROTEOMICS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84941031116     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00500     Document Type: Article

References (40)

1. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics Nature 2003, 422, 198-207 10.1038/nature01511
2. Deutsch, E. W.; Lam, H.; Aebersold, R. Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics Physiol. Genomics 2008, 33 (1) 18-25 10.1152/physiolgenomics.00298.2007
3. Desiere, F.; Deutsch, E. W.; Nesvizhskii, A. I.; Mallick, P.; King, N. L.; Eng, J. K.; Aderem, A.; Boyle, R.; Brunner, E.; Donohoe, S.; Fausto, N.; Hafen, E.; Hood, L.; Katze, M. G.; Kennedy, K. A.; Kregenow, F.; Lee, H.; Lin, B.; Martin, D.; Ranish, J. A.; Rawlings, D. J.; Samelson, L. E.; Shiio, Y.; Watts, J. D.; Wollscheid, B.; Wright, M. E.; Yan, W.; Yang, L.; Yi, E. C.; Zhang, H.; Aebersold, R. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry Genome Biol. 2004, 6 (1) R9 10.1186/gb-2004-6-1-r9
4. Deutsch, E. W.; Lam, H.; Aebersold, R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows EMBO Rep. 2008, 9 (5) 429-34 10.1038/embor.2008.56
5. Farrah, T.; Deutsch, E. W.; Omenn, G. S.; Campbell, D. S.; Sun, Z.; Bletz, J. A.; Mallick, P.; Katz, J. E.; Malmstrom, J.; Ossola, R.; Watts, J. D.; Lin, B.; Zhang, H.; Moritz, R. L.; Aebersold, R. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas Mol. Cell. Proteomics 2011, 10 (9) M110.006353 10.1074/mcp.M110.006353
6. 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 10.1021/pr301012j
7. 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
8. Bislev, S. L.; Deutsch, E. W.; Sun, Z.; Farrah, T.; Aebersold, R.; Moritz, R. L.; Bendixen, E.; Codrea, M. C. A Bovine PeptideAtlas of milk and mammary gland proteomes Proteomics 2012, 12 (18) 2895-9 10.1002/pmic.201200057
9. Bundgaard, L.; Jacobsen, S.; Sørensen, M. A.; Sun, Z.; Deutsch, E. W.; Moritz, R. L.; Bendixen, E. The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research Proteomics 2014, 14 (6) 763-73 10.1002/pmic.201300398
10. Vialas, V.; Sun, Z.; Loureiro y Penha, C. V.; Carrascal, M.; Abian, J.; Monteoliva, L.; Deutsch, E. W.; Aebersold, R.; Moritz, R. L.; Gil, C. A Candida albicans PeptideAtlas J. Proteomics 2014, 97, 62-8 10.1016/j.jprot.2013.06.020
11. Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats Mol. Syst. Biol. 2005, 1, E1-E8 10.1038/msb4100024
12. 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
13. 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
14. 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
15. Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 20 (9) 1466-7 10.1093/bioinformatics/bth092
16. MacLean, B.; Eng, J. K.; Beavis, R. C.; McIntosh, M. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine Bioinformatics 2006, 22 (22) 2830-2 10.1093/bioinformatics/btl379
17. Eng, J. K.; Jahan, T. A.; Hoopmann, M. R. Comet: an open-source MS/MS sequence database search tool Proteomics 2013, 13 (1) 22-4 10.1002/pmic.201200439
18. Apweiler, R.; Bairoch, A.; Wu, C. H.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M. J.; Natale, D. A.; O'Donovan, C.; Redaschi, N.; Yeh, L. S. UniProt: the Universal Protein knowledgebase Nucleic Acids Res. 2004, 32 (Database issue) 115D 10.1093/nar/gkh131
19. Uniprot Activities at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2014, 42 (Database issue) D191-8 10.1093/nar/gkt1140
20. Kersey, P. J.; Duarte, J.; Williams, A.; Karavidopoulou, Y.; Birney, E.; Apweiler, R. The International Protein Index: an integrated database for proteomics experiments Proteomics 2004, 4 (7) 1985-8 10.1002/pmic.200300721
21. Craig, R.; Cortens, J. P.; Beavis, R. C. Open source system for analyzing, validating, and storing protein identification data J. Proteome Res. 2004, 3 (6) 1234-42 10.1021/pr049882h
22. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74, 5383-5392 10.1021/ac025747h
23. Shteynberg, D.; Deutsch, E. W.; Lam, H.; Eng, J. K.; Sun, Z.; Tasman, N.; Mendoza, L.; Moritz, R. L.; Aebersold, R.; Nesvizhskii, A. I. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates Mol. Cell. Proteomics 2011, 10 (12) M111.007690 10.1074/mcp.M111.007690
24. 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
25. 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, mcp.M114.046995 10.1074/mcp.M114.046995
26. 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
27. Boeckmann, B.; Bairoch, A.; Apweiler, R.; Blatter, M. C.; Estreicher, A.; Gasteiger, E.; Martin, M. J.; Michoud, K.; O'Donovan, C.; Phan, I.; Pilbout, S.; Schneider, M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res. 2003, 31 (1) 365-70 10.1093/nar/gkg095
28. Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry Anal. Chem. 2003, 75, 4646-4658 10.1021/ac0341261
29. Ellis, M. J.; Gillette, M.; Carr, S. A.; Paulovich, A. G.; Smith, R. D.; Rodland, K. K.; Townsend, R. R.; Kinsinger, C.; Mesri, M.; Rodriguez, H.; Liebler, D. C. Clinical Proteomic Tumor Analysis, C., Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium Cancer Discovery 2013, 3 (10) 1108-12 10.1158/2159-8290.CD-13-0219
30. 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
31. 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
32. 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
33. Nesvizhskii, A. I. Proteogenomics: concepts, applications and computational strategies Nat. Methods 2014, 11 (11) 1114-25 10.1038/nmeth.3144
34. Glusman, G.; Caballero, J.; Mauldin, D. E.; Hood, L.; Roach, J. C. Kaviar: an accessible system for testing SNV novelty Bioinformatics 2011, 27 (22) 3216-7 10.1093/bioinformatics/btr540
35. Deutsch, E. W.; Mendoza, L.; Shteynberg, D.; Slagel, J.; Sun, Z.; Moritz, R. L. Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics Proteomics: Clin. Appl. 2015, n/a 10.1002/prca.201400164
36. Ezkurdia, I.; Vazquez, J.; Valencia, A.; Tress, M. Analyzing the First Drafts of the Human Proteome J. Proteome Res. 2014, 13 (8) 3854-3855 10.1021/pr500572z
37. Lefranc, M. P.; Giudicelli, V.; Ginestoux, C.; Jabado-Michaloud, J.; Folch, G.; Bellahcene, F.; Wu, Y.; Gemrot, E.; Brochet, X.; Lane, J.; Regnier, L.; Ehrenmann, F.; Lefranc, G.; Duroux, P. IMGT, the international ImMunoGeneTics information system Nucleic Acids Res. 2009, 37 (Database issue) D1006-12 10.1093/nar/gkn838
38. Picotti, P.; Bodenmiller, B.; Mueller, L. N.; Domon, B.; Aebersold, R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics Cell 2009, 138 (4) 795-806 10.1016/j.cell.2009.05.051
39. Kusebauch, U.; Deutsch, E. W.; Campbell, D. S.; Sun, Z.; Farrah, T.; Moritz, R. L. Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Current Protocols in Bioinformatics/Editoral Board, Andreas D. Baxevanis...[et al.], 2014; Vol. 46, pp 13251-132528.
40. 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