Automated Data Integration and Determination of Posttranslational Modifications with the Protein Inference Engine

Methods in Molecular Biology

Volumn 694, Issue , 2011, Pages 255-290

  Jefferys, Stuart R ^a   Giddings, Morgan C ^b  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

Bottom up; Data integration; MCMC; PIE; Proteomics; PTM; Simulated annealing; Top down

Indexed keywords

ISOPROTEIN; PEPTIDE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; INFORMATION PROCESSING; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; MOLECULAR WEIGHT; PHOSPHORYLATION; PROTEIN PROCESSING;

AMINO ACID SEQUENCE; AUTOMATIC DATA PROCESSING; COMPUTATIONAL BIOLOGY; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PEPTIDES; PHOSPHORYLATION; PROTEIN ISOFORMS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; SOFTWARE;

MLCS; MLOWN;

EID: 79952117653     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-977-2_17     Document Type: Chapter

References (35)

1. Seo, J. and Lee, K. J. (2004) Post-translational modifications and their biological functions: proteomic analysis and systematic approaches. J. Biochem. Mol. Biol. 37, 35–44.
2. Walsh, C. T., Garneau-Tsodikova, S., and Gatto, G. J. (2005) Protein posttranslational modifications: the chemistry of proteome diversifications. Angew. Chem. Int. Ed. Engl. 44, 7342–7372.
3. Kollmann, M., Lovdok, L., Bartholome, K., Timmer, J., and Sourjik, V. (2005) Design principles of a bacterial signaling network. Nature 438, 504–507.
4. Kentner, D. and Sourjik, V. (2006) Spatial organization of the bacterial chemotaxis system. Curr. Opin. Microbiol. 9, 619–624.
5. Shi, Y. (2007) Histone lysine demethylases: emerging roles in development, physiology and disease. Nat. Rev. Genet. 8, 829–833.
6. Minamoto, T., Buschmann, T., Habelhah, H., Matusevich, E., Tahara, H., Boerresen-Dale, A. L., et al. (2001) Distinct pattern of p53 phosphorylation in human tumors. Oncogene. 20, 3341–3347.
7. Banerjee, A. and Gerondakis, S. (2007) Coordinating TLR-activated signaling pathways in cells of the immune system. Immunol. Cell Biol. 85, 420–424.
8. Mann, M. and Jensen, O. N. (2003) Proteomic analysis of post-translational modifications. Nat. Biotechnol. 21, 255–261.
9. Domon, B. and Aebersold, R. (2006) Mass spectrometry and protein analysis. Science 312, 212–217.
10. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based
11. Craig, R. and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466–1467.
12. Little, D. P., Speir, J. P., Senko, M. W., O’Connor, P. B., and McLafferty, F. W. (1994). Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. Anal. Chem. 66, 2809–2815.
13. Kelleher, N. L., Zubarev, R. A., Bush, K., Furie, B., Furie, B. C., McLafferty, F. W., and Walsh, C. T. (1999) Localization of labile posttranslational modifications by electron capture dissociation: the case of gamma-carboxyglutamic acid. Anal. Chem. 71, 4250–4253.
14. Zubarev, R. A., Haselmann, K. F., Budnik, B., Kjeldsen, F., and Jensen, F. (2002) Toward and understanding of the mechanisms of elec-tron-capture dissociation: a historical perspective and modern ideas. Eur. J. Mass. Spectrom. 8, 337–349.
15. Siuti, N. and Kelleher, N. L. (2007) Decoding protein modifications using top-down mass spectrometry. Nat. Methods. 4, 817–821.
16. VerBerkmoes, N. C., Bundy, J. L., Hauser, L., Asano, K. G., Razumovskaya, J., Larimer, F., et al. (2002) Integrating “top-down” and “bottom-up” mass spectrometric approaches for proteomic analysis of Shewanella oneiden-sis. J. Proteome Res. 1, 239–252.
17. Strader, M. B., Verberkmoes, N. C., Tabb, D. L., Connelly, H. M., Barton, J. W., Bruce, B. D., et al. (2004) Characterization of the 70S ribosome from Rhodopseudomonas palustris using an integrated “top-down” and “bot-tom-up” mass spectrometric approach. J. Proteome Res. 3, 965–978.
18. Yu, Y., Ji, H., Doudna, J. A., and Leary, J. A. (2005) Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes. Protein Sci. 14, 1438–1446.
19. Kertesz, V., Connelly, H. M., Erickson, B. K., and Hettich, R. L. (2009) PTMSearchPlus: software tool for automated protein identification and post-translational modification characterization by integrating accurate intact protein mass and bottom-up mass spectrometric data searches. Anal. Chem. 81, 8387–8395.
20. Wilkins, M. R., Gasteiger, E., Gooley, A. A., Herbert, B. R., Molloy, M. P., Binz, P. A., et al. (1999) High-throughput mass spectrometric discovery of protein post-translational modifications. J. Mol. Biol. 289, 645–657.
21. Blom, N., Gammeltoft, S., and Brunak, S. (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294, 1351–1362.
22. Monigatti, F., Gasteiger, E., Bairoch, A., and Jung, E. (2002) The sulfinator: predicting tyrosine sulfation sites in protein sequences. Bioinformatics 18, 769–770.
23. Bendtsen, J. D., Nielsen, H., von Heijne, G., and Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783–795.
24. Frottin, F., Martinez, A., Peynot, P., Mitra, S., Holz, R. C., Giglione, C., and Meinnel, T. (2006) The proteomics of N-terminal methionine cleavage. Mol. Cell. Proteomics 51, 2336–2349.
25. Metropolis, N., Rosenbluth, A. W, Rosenbluth, M. N., Teller, A. H., and Teller, E. (1953) Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087–1092.
26. Kirkpatrick, S., Gelatt, C. D., and Vecchi, M. P. (1983) Optimization by simulated annealing. Science 220, 671–680.
27. Brocchieri, L. and Karlin, S. (2005). Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res. 33, 3390–3400.
28. Hastings, W. K. (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57, 97–109.
29. Huelsenbeck, J. P., Ronquist, F., Nielsen, R., and Bollback, J. P. (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310–2314.
30. Holmes, M. R. and Giddings, M. C. (2004) Prediction of posttranslational modifications using intact-protein mass spectrometric data. Anal. Chem. 76, 276–282.
31. Creasy, D. M. and Cottrell, J. S. (2004) Unimod: protein modifications for mass spectrometry. Proteomics 4, 1534–1536.
32. Wisz, M. S, Suarez, M. K, Holmes, M. R, and Giddings, M. C. (2004) GFSWeb: a web tool for genome-based identification of proteins from mass spectrometric samples. J. Proteome Res. 3, 1292–1295.
33. Searle, B. C, Dasari, S., Wilmarth, P. A., Turner, M., Reddy, A. P., David, L. L., and Nagalla, S. R. (2005) Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm. J. Proteome Res. 4, 546–554.
34. Gotoh, O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol. 162, 705–708.
35. Lee, T. Y., Huang, H. D., Hung, J. H. Huang, H. Y., Yang, Y. S., and Wang, T. H. (2006) dbPTM: an information repository of protein posttranslational modification. Nucleic Acids Res. 34, D622–D627.