Enhanced peptide identification by electron transfer dissociation using an improved mascot percolator

Molecular and Cellular Proteomics

Volumn 11, Issue 8, 2012, Pages 478-491

  Wright, James C ^a   Collins, Mark O ^a   Yu, Lu ^a   Käll, Lukas ^b   Brosch, Markus ^a   Choudhary, Jyoti S ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; COMPUTER PROGRAM; ELECTRON TRANSPORT; FALSE POSITIVE RESULT; MACHINE LEARNING; MASCOT PERCOLATOR; PRIORITY JOURNAL; PROTEIN ANALYSIS; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FUNGAL PROTEINS; HUMANS; PEPTIDES; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE; TANDEM MASS SPECTROMETRY; YEASTS;

EID: 84864815807     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O111.014522     Document Type: Article

References (37)

1. Appella, E., and Anderson, C. W. (2007) New prospects for proteomics-electron-capture (ECD) and electron-transfer dissociation (ETD) fragmentation techniques and combined fractional diagonal chromatography (COFRADIC). Febs J. 274, 6255
2. Käll, L., Canterbury, J. D., Weston, J., Noble, W. S., and MacCoss, M. J. (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4, 923-925
3. Brosch, M., Yu, L., Hubbard, T., and Choudhary, J. (2009) Accurate and sensitive peptide identification with Mascot Percolator. J. Proteome Res. 8, 3176-3181
4. Good, D. M., Wirtala, M., McAlister, G. C., and Coon, J. J. (2007) Performance characteristics of electron transfer dissociation mass spectrometry. Mol. Cell. Proteomics 6, 1942-1951
5. Mikesh, L. M., Ueberheide, B., Chi, A., Coon, J. J., Syka, J. E., Shabanowitz, J., and Hunt, D. F. (2006) The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta 1764, 1811-1822
6. Zubarev, R. A. (2004) Electron-capture dissociation tandem mass spectrometry. Curr. Opin. Biotechnol. 15, 12-16
7. Chi, A., Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., and Hunt, D. F. (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 104, 2193-2198
8. Domon, B., Bodenmiller, B., Carapito, C., Hao, Z., Huehmer, A., and Aebersold, R. (2009) Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome. J. Proteome Res. 8, 2633-2639
9. Molina, H., Horn, D. M., Tang, N., Mathivanan, S., and Pandey, A. (2007) Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 104, 2199-2204
10. Wiesner, J., Premsler, T., and Sickmann, A. (2008) Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 8, 4466-4483
11. McAlister, G. C., Berggren, W. T., Griep-Raming, J., Horning, S., Makarov, A., Phanstiel, D., Stafford, G., Swaney, D. L., Syka, J. E., Zabrouskov, V., and Coon, J. J. (2008) A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J. Proteome Res. 7, 3127-3136
12. Nagaraj, N., D'Souza, R. C., Cox, J., Olsen, J. V., and Mann, M. (2010) Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J. Proteome Res. 9, 6786-6794
13. Biemann, K. (1990) Sequencing of peptides by tandem mass-spectrometry and high-energy collision-induced dissociation. Methods Enzymol. 193, 455-479
14. 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
15. Hart, S. R., Lau, K. W., Gaskell, S. J., and Hubbard, S. J. (2011) Distributions of ion series in ETD and CID spectra: making a comparison. Methods Mol. Biol. 696, 327-337
16. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567
17. Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., and Bryant, S. H. (2004) Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964
18. Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467
19. Kandasamy, K., Pandey, A., and Molina, H. (2009) Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Anal. Chem. 81, 7170-7180
20. Sweet, S. M., Jones, A. W., Cunningham, D. L., Heath, J. K., Creese, A. J., and Cooper, H. J. (2009) Database search strategies for proteomic data sets generated by electron capture dissociation mass spectrometry. J. Proteome Res. 8, 5475-5484
21. Good, D. M., Wenger, C. D., and Coon, J. J. (2010) The effect of interfering ions on search algorithm performance for electron-transfer dissociation data. Proteomics 10, 164-167
22. Baker, P. R., Medzihradszky, K. F., and Chalkley, R. J. (2010) Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring. Mol. Cell. Proteomics 9, 1795-1803
23. Deutsch, E. W., Shteynberg, D., Lam, H., Sun, Z., Eng, J. K., Carapito, C., von Haller, P. D., Tasman, N., Mendoza, L., Farrah, T., and Aebersold, R. (2010) Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. Proteomics 10, 1190-1195
24. Liu, X., Shan, B., Xin, L., and Ma, B. (2010) Better score function for peptide identification with ETD MS/MS spectra. BMC Bioinformatics 11 Suppl 1, S4
25. Sadygov, R. G., Good, D. M., Swaney, D. L., and Coon, J. J. (2009) A new probabilistic database search algorithm for ETD spectra. J. Proteome Res. 8, 3198-3205
26. Chalkley, R. J., Baker, P. R., Medzihradszky, K. F., Lynn, A. J., and Burlingame, A. L. (2008) In-depth analysis of tandem mass spectrometry data from disparate instrument types. Mol. Cell. Proteomics 7, 2386-2398
27. Swaney, D. L., McAlister, G. C., and Coon, J. J. (2008) Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat. Methods 5, 959-964
28. Käll, L., Storey, J. D., MacCoss, M. J., and Noble, W. S. (2008) Posterior error probabilities and false discovery rates: two sides of the same coin. J. Proteome Res. 7, 40-44
29. 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
30. Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I., Mallick, P., Eng, J., Chen, S., Eddes, J., Loevenich, S. N., and Aebersold, R. (2006) The PeptideAtlas project. Nucleic Acids Res. 34, D655-D658
31. Swaney, D. L., McAlister, G. C., Wirtala, M., Schwartz, J. C., Syka, J. E., and Coon, J. J. (2007) Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal. Chem. 79, 477-485
32. Vizcaino, J. A., Côté, R., Reisinger, F., Foster, J. M., Mueller, M., Rameseder, J., Hermjakob, H., and Martens, L. (2009) A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 9, 4276-4283
33. Spivak, M., Weston, J., Bottou, L., Käll, L., and Noble, W. S. (2009) Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets. J. Proteome Res. 8, 3737-3745
34. Klimek, J., Eddes, J. S., Hohmann, L., Jackson, J., Peterson, A., Letarte, S., Gafken, P. R., Katz, J. E., Mallick, P., Lee, H., Schmidt, A., Ossola, R., Eng, J. K., Aebersold, R., and Martin, D. B. (2008) The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J. Proteome Res. 7, 96-103
35. Granholm, V., Noble, W. S., and Kall, L. (2011) On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics. J. Proteome Res. 10, 3844
36. Wenger, C. D., Phanstiel, D. H., Lee, M. V., Bailey, D. J., and Coon, J. J. (2011) COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA. Proteomics 11, 1064-1074
37. Molina, H., Matthiesen, R., Kandasamy, K., and Pandey, A. (2008) Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Anal. Chem. 80, 4825-4835