Inference and validation of protein identifications

Molecular and Cellular Proteomics

Volumn 11, Issue 11, 2012, Pages 1097-1104

  Claassen, Manfred ^a  

^a Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

AMINO ACID SEQUENCE; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; FRAGMENTATION REACTION; PARSIMONY ANALYSIS; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN INFERENCE; PROTEIN TARGETING; PROTEOMICS; QUALITY CONTROL; REVIEW; STATISTICAL SIGNIFICANCE; VALIDATION PROCESS;

ANIMALS; GUIDELINES AS TOPIC; HUMANS; PROTEINS; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 84869211929     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.R111.014795     Document Type: Review

References (75)

1. Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J. F., Dougherty, B. A., Merrick, J. M., McKenney, K., Sutton, G., FitzHugh, W., Fields, C., Gocayne, J. D., Scott, J., Shirley, R., Liu, L.-I., Glodek, A., Kelley, J. M., Weidman, J. F., Phillips, C. A., Spriggs, T., Hedblom, E., Cotton, M. D., Utterback, T. R., Hanna, M. C., Nguyen, D. T., Saudek, D. M., Brandon, R. C., Fine, L. D., Fritchman, J. L., Fuhrmann, J. L., Geoghagen, N. S. M., Gnehm, C. L., McDonald, L. A., Small, K. V., Fraser, C. M., Smith, H. O., and Venter, J. C. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512
2. Hunt, D. F., Yates, J. R., 3rd, Shabanowitz, J., Winston, S., and Hauer, C. R. (1986) Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 83, 6233-6237 (Pubitemid 17174712)
3. Cormen, T. H. (2009) Introduction to algorithms. 3rd ed., MIT Press
4. McLafferty, F. W. (1981) Tandem mass spectrometry. Science 214, 280-287
5. Zubarev, R. A., Horn D. M., Fridriksson, E. K., Kelleher, N. L., Kruger, N. A., Lewis, M. A., Carpenter, B. K., and McLafferty, F. W. (2000) Electron capture dissociation for structural characterization of multiply charged protein cations. Anal. Chem. 72, 563-573 (Pubitemid 33595293)
6. Syka, J. E., Coon, J. J., Schroeder, M. J., Shabanowitz, J., and Hunt, D. F. (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 101, 9528-9533 (Pubitemid 38869270)
7. Nesvizhskii, A. I., and Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440
8. Shen, C., Wang, Z., Shankar, G., Zhang, X., and Li, L. (2008) A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry. Bioinformatics 24, 202-208
9. Eng, J. K., McCormack, A. L., and Yates Iii, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
10. Wysocki, V. H., Tsaprailis, G., Smith, L. L., and Breci, L. A. (2000) Mobile and localized protons: a framework for understanding peptide dissociation. J. Mass Spectrom. 35, 1399-1406 (Pubitemid 32063646)
11. Tabb, D. L., Smith, L. L., Breci, L. A., Wysocki, V. H., Lin, D., and Yates, J. R. 3rd (2003) Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal. Chem. 75, 1155-1163 (Pubitemid 36402645)
12. Michalski, A., Cox, J., and Mann, M. (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 10, 1785-1793
13. Mallick, P., Schirle, M., Chen, S. S., Flory, M. R., Lee, H., Martin, D., Ranish, J., Raught, B., Schmitt, R., Werner, T., Kuster, B., and Aebersold, R. (2007) Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25, 125-131 (Pubitemid 46098780)
14. Li, Y. F., Arnold, R. J., Tang, H., and Radivojac, P. (2010) The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics. J. Proteome Res. 9, 6288-6297
15. Taylor, J. A., and Johnson, R. S. (2001) Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal. Chem. 73, 2594-2604 (Pubitemid 32880663)
16. Ma, B., Zhang, K., Hendrie, C., Liang, C., Li, M., Doherty-Kirby, A., and Lajoie, G. (2003) PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom. 17, 2337-2342 (Pubitemid 37243319)
17. Frank, A., and Pevzner, P. (2005) PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem. 77, 964-973 (Pubitemid 40261761)
18. Fischer, B., Roth, V., Roos, F., Grossmann, J., Baginsky, S., Widmayer, P., Gruissem, W., and Buhmann, J. M. (2005) NovoHMM: a hidden Markov model for de novo peptide sequencing. Anal. Chem. 77, 7265-7273 (Pubitemid 41681392)
19. Mann, M., and Wilm, M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66, 4390-4399 (Pubitemid 124006101)
20. Nesvizhskii, A. I. (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteomics 73, 2092-2123
21. Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., and Apweiler, R. (2005) PRIDE: the proteomics identifications database. Proteomics 5, 3537-3545 (Pubitemid 41192059)
22. Brunner, E., Ahrens, C. H., Mohanty, S., Baetschmann, H., Loevenich, S., Potthast, F., Deutsch, E. W., Panse, C., de Lichtenberg, U., Rinner, O., Lee, H., Pedrioli, P. G., Malmstrom, J., Koehler, K., Schrimpf, S., Krijgsveld, J., Kregenow, F., Heck, A. J., Hafen, E., Schlapbach, R., and Aebersold, R. (2007) A high-quality catalog of the Drosophila melanogaster proteome. Nat. Biotechnol. 25, 576-583 (Pubitemid 46834841)
23. Baerenfaller, K., Grossmann, J., Grobei, M. A., Hull, R., Hirsch-Hoffmann, M., Yalovsky, S., Zimmermann, P., Grossniklaus, U., Gruissem, W., and Baginsky, S. (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320, 938-941 (Pubitemid 351929590)
24. Schrimpf, S. P., Weiss, M., Reiter, L., Ahrens, C. H., Jovanovic, M., Malmström, J., Brunner, E., Mohanty, S., Lercher, M. J., Hunziker, P. E., Aebersold, R., von Mering, C., and Hengartner, M. O. (2009) Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol. 7, e48
25. States, D. J., Omenn, G. S., Blackwell, T. W., Fermin, D., Eng, J., Speicher, D. W., and Hanash, S. M. (2006) Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 24, 333-338 (Pubitemid 43372157)
26. Zhang, B., Chambers, M. C., and Tabb, D. L. (2007) Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J. Proteome Res. 6, 3549-3557 (Pubitemid 47522746)
27. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658 (Pubitemid 37082259)
28. Eriksson, J., and Fenyö, D. (2003) Probity: a protein identification algorithm with accurate assignment of the statistical significance of the results. J. Proteome Res. 3, 32-36 (Pubitemid 38233447)
29. Serang, O., MacCoss, M. J., and Noble, W. S. (2010) Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. J. Proteome Res. 9, 5346-5357
30. Sadygov, R. G., Liu, H., and Yates, J. R. (2004) Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal. Chem. 76, 1664-1671 (Pubitemid 38338411)
31. Shteynberg, D., Deutsch, E. W., Lam, H., Eng, J. K., Sun, Z., Tasman, N., Mendoza, L., Moritz, R. L., Aebersold, R., and Nesvizhskii, A. I. (2011) iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol. Cell. Proteomics 10, 10.1074/mcp.M111.007690
32. Bandeira, N., Clauser, K. R., and Pevzner, P. A. (2007) Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol. Cell. Proteomics 6, 1123-1134 (Pubitemid 47099224)
33. Gerster, S., Qeli, E., Ahrens, C. H., and Buhlmann, P. (2010) Protein and gene model inference based on statistical modeling in k-partite graphs. Proc. Natl. Acad. Sci. U. S. A. 107, 12101-12106
34. Li, Y. F., Arnold, R.J., Li, Y., Radivojac, P., Sheng, Q., and Tang, H. (2009) A Bayesian approach to protein inference problem in shotgun proteomics. J. Computational Biol. 16, 1183-1193
35. Tang, H., Arnold, R. J., Alves, P., Xun, Z., Clemmer, D. E., Novotny, M. V., Reilly, J. P., and Radivojac, P. (2006) A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 22, e481-488 (Pubitemid 44288319)
36. Alves, P., Arnold, R. J., Novotny, M. V., Radivojac, P., Reilly, J. P., and Tang, H. (2007) Advancement in protein inference from shotgun proteomics using peptide detectability. Pacific Symposium on Biocomputing 12, 409-470
37. Koskinen, V. R., Emery, P. A., Creasy, D. M., and Cottrell, J. S. (2011) Hierarchical clustering of shotgun proteomics data. Mol. Cell. Proteomics 10, M110 003822
38. Yang, X., Dondeti, V., Dezube, R., Maynard, D. M., Geer, L. Y., Epstein, J., Chen, X., Markey, S. P., and Kowalak, J. A. (2004) DBParser: web-based software for shotgun proteomic data analyses. J. Proteome Res. 3, 1002-1008 (Pubitemid 39425657)
39. Ma, Z. Q., Dasari, S., Chambers, M. C., Litton, M. D., Sobecki, S. M., Zimmerman, L. J., Halvey, P. J., Schilling, B., Drake, P. M., Gibson, B. W., and Tabb, D. L. (2009) IDPicker 2.0: improved protein assembly with high discrimination peptide identification filtering. J. Proteome Res. 8, 3872-3881
40. Gupta, N., and Pevzner, P. A. (2009) False discovery rates of protein identifications: a strike against the two-peptide rule. J. Proteome Res. 8, 4173-4181
41. Grobei, M. A., Qeli, E., Brunner, E., Rehrauer, H., Zhang, R., Roschitzki, B., Basler, K., Ahrens, C. H., and Grossniklaus, U. (2009) Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function. Genome Res. 19, 1786-1800
42. Farrah, T., Deutsch, E. W., Omenn, G. S., Campbell, D. S., Sun, Z., Bletz, J. A., Mallick, P., Katz, J. E., Malmstro?m, J., Ossola, R., Watts, J. D., Lin, B., Zhang, H., Moritz, R. L., and Aebersold, R. (2011) A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol. Cell. Proteomics 10, 10.1074/mcp.M110. 006353
43. Claassen, M., Reiter, L., Hengartner, M. O., Buhmann, J. M., and Aebersold, R. (2012) Generic comparison of protein inference engines. Mol. Cell. Proteomics 11, 10.1074/mcp.O110.007088
44. Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statistical Soc. 57, 289-300
45. Storey, J. D., and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U. S. A. 100, 9440-9445 (Pubitemid 37033947)
46. Alves, G., Ogurtsov, A. Y., Wu, W. W., Wang, G., Shen, R. F., and Yu, Y. K. (2007) Calibrating E-values for MS2 database search methods. Biol. Direct 2, 26
47. Gupta, N., Bandeira, N., Keich, U., and Pevzner, P. A. (2011) Target-decoy approach and false discovery rate: when things may go wrong. J. Am. Soc. Mass Spectrom. 22, 1111-1120
48. Kim, S., Gupta, N., and Pevzner, P. A. (2008) Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res. 7, 3354-3363
49. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392 (Pubitemid 35215372)
50. Dempster, A. P., Laird, N. M., and Rubin, D. B. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. Roy. Statistical Soc. 39, 1-38
51. Moore, R. E., Young, M. K., and Lee, T. D. (2002) Qscore: an algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom. 13, 378-386 (Pubitemid 34280088)
52. Elias, J. E., and Gygi, S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214 (Pubitemid 46358868)
53. Reiter, L., Claassen, M., Schrimpf, S. P., Jovanovic, M., Schmidt, A., Buhmann, J. M., Hengartner, M. O., and Aebersold, R. (2009) Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol. Cell. Proteomics 8, 2405-2417
54. Price, T. S., Lucitt, M. B., Wu, W., Austin, D. J., Pizarro, A., Yocum, A. K., Blair, I. A., FitzGerald, G. A., and Grosser, T. (2007) EBP, a program for protein identification using multiple tandem mass spectrometry datasets. Mol. Cell. Proteomics 6, 527-536 (Pubitemid 46554546)
55. Nesvizhskii, A. I., Vitek, O., and Aebersold, R. (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 4, 787-797 (Pubitemid 350055575)
56. Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., and Aebersold, R. (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795-806
57. de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., and Mann, M. (2008) Comprehensive mass-spectrometry- based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254
58. Castellana, N., and Bafna, V. (2010) Proteogenomics to discover the full coding content of genomes: a computational perspective. J. Proteomics 73, 2124-2135
59. Ansong, C., Purvine, S. O., Adkins, J. N., Lipton, M. S. and Smith, R. D. (2008) Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Briefings Functional Genomics Proteomics 7, 50-62 (Pubitemid 351721150)
60. Bitton, D. A., Smith, D. L., Connolly, Y., Scutt, P. J., and Miller, C. J. (2010) An integrated mass-spectrometry pipeline identifies novel protein cod-ing- regions in the human genome. PloS one 5, e8949
61. 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., and Aebersold, R. (2005) Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 6, R9
62. Fermin, D., Allen, B. B., Blackwell, T. W., Menon, R., Adamski, M., Xu, Y., Ulintz, P., Omenn, G. S., and States, D. J. (2006) Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol. 7, R35
63. Loevenich, S. N., Brunner, E., King, N. L., Deutsch, E. W., Stein, S. E., FlyBase Consortium, Aebersold, R., and Hafen, E. (2009) The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC Bioinformatics 10, 59
64. Merrihew, G. E., Davis, C., Ewing, B., Williams, G., Käll, L., Frewen, B. E., Noble, W. S., Green, P., Thomas, J. H., and MacCoss, M. J. (2008) Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res. 18, 1660-1669
65. Tanner, S., Shen, Z., Ng, J., Florea, L., Guigó, R., Briggs, S. P., and Bafna, V. (2007) Improving gene annotation using peptide mass spectrometry. Genome Res. 17, 231-239 (Pubitemid 46220768)
66. Edwards, N. J. (2007) Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Mol. Syst. Biol. 3, 102
67. Roos, F. F., Jacob, R., Grossmann, J., Fischer, B., Buhmann, J. M., Gruissem, W., Baginsky, S., and Widmayer, P. (2007) PepSplice: cacheefficient search algorithms for comprehensive identification of tandem mass spectra. Bioinformatics 23, 3016-3023 (Pubitemid 350162866)
68. Kuster, B., Mortensen, P., Andersen, J. S., and Mann, M. (2001) Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 1, 641-650 (Pubitemid 33588315)
69. Shafer, P., Lin, D. M., and Yona, G. (2006) EST2Prot: mapping EST sequences to proteins. BMC Genomics 7, 41
70. Eriksson, J., and Fenyo, D. (2007) Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs. Nat. Biotechnol. 25, 651-655 (Pubitemid 46897209)
71. Schmidt, A., Claassen, M., and Aebersold, R. (2009) Directed mass spectrometry: towards hypothesis-driven proteomics. Curr. Opinion Chem. Biol. 13, 510-517
72. Schmidt, A., Gehlenborg, N., Bodenmiller, B., Mueller, L. N., Campbell, D., Mueller, M., Aebersold, R., and Domon, B. (2008) An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol. Cell. Proteomics 7, 2138-2150
73. Zerck, A., Nordhoff, E., Resemann, A., Mirgorodskaya, E., Suckau, D., Reinert, K., Lehrach, H., and Gobom, J. (2009) An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics. J. Proteome Res. 8, 3239-3251
74. Claassen, M., Aebersold, R., and Buhmann, J. M. (2009) Proteome coverage prediction with infinite Markov models. Bioinformatics 25, i154-160
75. Claassen, M., Aebersold, R., and Buhmann, J. M. (2011) Proteome coverage prediction for integrated proteomics datasets. J. Computational Biol. 18, 283-293