A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry

Molecular and Cellular Proteomics

Volumn 9, Issue 5, 2010, Pages 764-779

  Baliban, Richard C ^a   DiMaggio, Peter A ^a   Plazas Mayorca, Mariana D ^b   Young, Nicolas L ^b   Garcia, Benjamin A ^b   Floudas, Christodoulos A ^a  

^a Princeton University   (United States)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; HISTONE H3; ISOTOPE; PHOSPHOPEPTIDE;

ALGORITHM; ARTICLE; CHROMATIN; COLLISIONALLY ACTIVATED DISSOCIATION; ELECTRON CAPTURE DETECTION; ELECTRON TRANSPORT; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROCESSING; TANDEM MASS SPECTROMETRY;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; HELA CELLS; HISTONES; HUMANS; MICE; MOLECULAR SEQUENCE DATA; PHOSPHOPEPTIDES; PROTEIN PROCESSING, POST-TRANSLATIONAL; REPRODUCIBILITY OF RESULTS; TANDEM MASS SPECTROMETRY;

EID: 77951870981     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M900487-MCP200     Document Type: Article

References (63)

1. 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)
2. Witze, E. S., Old, W. M., Resing, K. A., and Ahn, N. G. (2007) Mapping protein post-translational modifications with mass spectrometry. Nat. Methods 4, 798-806 (Pubitemid 350055576)
3. 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)
4. Tanner, S., Shu, H., Frank, A., Wang, L. C., Zandi, E., Mumby, M., Pevzner, P. A., and Bafna, V. (2005) InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 77, 4626-4639 (Pubitemid 41542287)
5. 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 (Pubitemid 40548162)
6. Matthiesen, R., Trelle, M. B., Højrup, P., Bunkenborg, J., and Jensen, O. N. (2005) VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J. Proteome Res. 4, 2338-2347 (Pubitemid 41814304)
7. Kim, S., Na, S., Sim, J. W., Park, H., Jeong, J., Kim, H., Seo, Y., Seo, J., Lee, K. J., and Paek, E. (2006) Modi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra. Nucleic Acids Res. 34, W258-W263 (Pubitemid 44529775)
8. Savitski, M. M., Nielsen, M. L., and Zubarev, R. A. (2006) ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures. Mol. Cell. Proteomics 5, 935-948
9. Zamdborg, L., LeDuc, R. D., Glowacz, K. J., Kim, Y. B., Viswanathan, V., Spaulding, I. T., Early, B. P., Bluhm, E. J., Babai, S., and Kelleher, N. L. (2007) Prosight PTM 2.0: improved protein identification and characterization for top down mass spectrometry. Nucleic Acids Res. 35, W701-W706
10. Yates, J. R., 3rd, Eng, J. K., McCormack, A. L., and Schieltz, D. (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426-1436
11. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching databases using mass spectrometry data. Electrophoresis 20, 3551-3567
12. Lu, B., and Chen, T. (2003) A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications. Bioinformatics 19, ii113-ii121
13. 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 (Pubitemid 39425651)
14. Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467 (Pubitemid 38931421)
15. Shadforth, I., Xu, W., Crowther, D., and Bessant, C. (2006) GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra. J. Proteome Res. 5, 2849-2852 (Pubitemid 44595185)
16. Baumgartner, C., Rejtar, T., Kullolli, M., Akella, L. M., and Karger, B. L. (2008) SeMoP: a new computational strategy for the unrestricted search for modified peptides using LC-MS/MS data. J. Proteome Res. 7, 4199-4208
17. Liu, C., Yan, B., Song, Y., Xu, Y., and Cai, L. (2006) Peptide sequence tag-based blind identification of post-translational modifications with point process model. Bioinformatics 22, e307-e313
18. Seo, J., Jeong, J., Kim, Y. M., Hwang, N., Paek, E., and Lee, K. J. (2008) Strategy for Comprehensive identification of post-translational modifications in cellular proteins, including low abundant modifications: application to glyceraldehyde-3-phosphate dehydrogenase. J. Proteome Res. 7, 587-602 (Pubitemid 351294021)
19. Hansen, B. T., Davey, S. W., Ham, A. J., and Liebler, D. C. (2005) P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data. J. Proteome Res. 4, 358-368
20. DiMaggio, P. A., Jr., Young, N. L., Baliban, R. C., Garcia, B. A., and Floudas, C. A. (2009) A mixed-integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed ETD tandem mass spectrometry Mol. Cell. Proteomics 8, 2527-2543
21. Havilio, M., and Wool, A. (2007) Large-scale unrestricted identification of post-translational modifications using tandem mass spectrometry. Anal. Chem. 79, 1362-1368 (Pubitemid 46309627)
22. Chen, Y., Chen, W., Cobb, M. H., and Zhao, Y. (2009) PTMap - a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. Proc. Natl. Acad. Sci. U.S.A. 106, 761-766
23. 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
24. Zhang, N., Aebersold, R., and Schwikowski, B. (2002) ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectrometry. Proteomics 2, 1406-1412 (Pubitemid 35340021)
25. Agilent (2004) Spectrum Mill for MassHunter Workstation, Agilent, Santa Clara, CA
26. Colinge, J., Masselot, A., Giron, M., Dessingy, T., and Magnin, J. (2003) OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 3, 1454-1463 (Pubitemid 37048071)
27. Tabb, D. L., Fernando, C. G., and Chambers, M. C. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res. 6, 654-661
28. Hernandez, P., Gras, R., Frey, J., and Appel, R. D. (2003) Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data. Proteomics 3, 870-878 (Pubitemid 36801673)
29. Creasy, D. M., and Cottrell, J. S. (2004) Unimod: protein modifications for mass spectrometry. Proteomics 4, 1534-1536 (Pubitemid 38738312)
30. Garavelli, J. S. (2004) The RESID database of protein modifications as a resource and annotation tool. Proteomics 4, 1527-1533
31. Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., and Mann, M. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635-648 (Pubitemid 44647421)
32. 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)
33. 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 (Pubitemid 44895029)
34. Udeshi, N. D., Shabanowitz, J., Hunt, D. F., and Rose, K. L. (2007) Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS. FEBS J. 274, 6269-6276 (Pubitemid 350215921)
35. Zubarev, R. A., Kelleher, N. L., and McLafferty, F. W. (1998) Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 120, 3265-3266
36. Bakhtiar, R., and Guan, Z. (2006) Electron capture dissociation mass spectrometry in characterization of peptides and proteins. Biotechnol. Lett. 28, 1047-1059
37. Good, D. M., Wenger, C. D., McAlister, G. C., Bai, D. L., Hunt, D. F., and Coon, J. J. (2009) Post-acquisition ETD spectral processing for increased peptide identifications. J. Am. Soc. Mass Spectrom. 20, 1435-1440
38. 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
39. Craig, R., and Beavis, R. C. (2003) A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun. Mass Spectrom. 17, 2310-2316 (Pubitemid 37243315)
40. Creasy, D. M., and Cottrell, J. S. (2002) Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics 2, 1426-1434 (Pubitemid 35340023)
41. Tanner, S., Pevzner, P. A., and Bafna, V. (2006) Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nat. Protoc. 1, 67-72
42. Tsur, D., Tanner, S., Zandi, E., Bafna, V., and Pevzner, P. A. (2005) Identification of post-translational modifications by blind search of mass spectra. Nat. Biotechnol. 23, 1562-1567 (Pubitemid 41752935)
43. Kim, S., Bandeira, N., and Pevzner, P. A. (2009) Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification. Mol. Cell. Proteomics 8, 1391-1400
44. Dimaggio, P. A., and Floudas, C. A. (2007) A mixed-integer optimization framework for de novo peptide identification. AIChE J. 53, 160-173 (Pubitemid 46114027)
45. DiMaggio, P. A., Jr., and Floudas, C. A. (2007) De novo peptide identification via tandem mass spectrometry and integer linear optimization. Anal. Chem. 79, 1433-1446 (Pubitemid 46309634)
46. DiMaggio, P. A., Jr., Floudas, C. A., Lu, B., and Yates, J. R., 3rd (2008) A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or orbitrap tandem mass spectrometry. J. Proteome Res. 7, 1584-1593
47. Garcia, B. A., Pesavento, J. J., Mizzen, C. A., and Kelleher, N. L. (2007) Pervasive combinatorial modification of histone H3 in human cells. Nat. Methods 4, 487-489 (Pubitemid 46852073)
48. Garcia, B. A., Mollah, S., Ueberheide, B. M., Busby, S. A., Muratore, T. L., Shabanowitz, J., and Hunt, D. F. (2007) Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protoc. 2, 933-938 (Pubitemid 46745589)
49. Shiio, Y., Eisenman, R. N., Yi., E. C., Donohoe, S., Goodlett, D. R., and Aebersold, R. (2003) Quantitative proteomic analysis of chromatin-associated factors. J. Am. Soc. Mass Spectrom. 14, 696-703 (Pubitemid 36870952)
50. El Gazzar, M., Yoza, B. K., Chen, X., Garcia, B. A., Young, N. L., and McCall, C. E. (2009) Chromatin-specific remodeling by HMGB1 and linker histone H1 silences proinflammatory genes during endotoxin tolerance. Mol. Cell. Biol. 29, 1959-1971
51. Purvine, S., Kolker, N., and Kolker, E. (2004) Spectral quality assessment for high throughput tandem mass spectrometry proteomics. OMICS 8, 255-265 (Pubitemid 39425675)
52. Prince, J. T., Carlson, M. W., Wang, R., Lu, P., and Marcotte, E. M. (2004) The need for a public proteomics repository. Nat. Biotechnol. 22, 471-472
53. 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)
54. Hubler, S. L., Jue, A., Keith, J., McAlister, G. C., Craciun, G., and Coon, J. J. (2008) Valence parity renders z(*)-type ions chemically distinct. J. Am. Chem. Soc. 130, 6388-6394 (Pubitemid 351711193)
55. IBM ILOG (2008) ILOG CPLEX C++ API 11.1 Reference Manual, IBM ILOG, Armonk, NY
56. Floudas, C. A. (1995) Nonlinear and Mixed-Integer Optimization, Oxford University Press, New York
57. Nemhauser, G. L., and Wolsey, L. A. (1988) Integer and Combinatorial Optimization, John Wiley and Sons, Inc., New York
58. Floudas, C. A., and Paules, G. E., 4th (1988) A mixed-integer nonlinear programming formulation for the synthesis of heat-integrated distillation sequences. Comp. Chem. Eng. 12, 531-546
59. Kokossis, A. C., and Floudas, C. A. (1991) Synthesis of isothermal reactor-separator-recycle systems. Chem. Eng. Sci. 46, 1361-1383
60. Kokossis, A. C., and Floudas, C. A. (1994) Optimization of complex reactor networks - II: nonisothermal operation. Chem. Eng. Sci. 49, 1037-1051
61. Floudas, C. A., and Anastasiadis, S. H. (1988) Synthesis of general distillation sequences with several multicomponent feeds and products. Chem. Eng. Sci. 43, 2407-2419
62. Ciric, A. R., and Floudas, C. A. (1989) A retrofit approach for heat exchanger networks. Comp. Chem. Eng. 13, 703-715
63. Kinter, M., and Sherman, N. E. (2000) Protein Sequencing and Identification Using Tandem Mass Spectrometry, John Wiley & Sons, Inc., New York