Spectral dictionaries. Integrating de novo peptide sequencing with database search of tandem mass spectra

Molecular and Cellular Proteomics

Volumn 8, Issue 1, 2009, Pages 53-69

  Kim, Sangtae ^a   Gupta, Nitin ^b   Bandeira, Nuno ^a   Pevzner, Pavel A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; GENOME ANALYSIS; GENOMICS; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEOMICS; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE DATA; PEPTIDES; SEQUENCE ANALYSIS, PROTEIN; SHEWANELLA; TANDEM MASS SPECTROMETRY;

EID: 59149096107     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M800103-MCP200     Document Type: Article

References (53)

1. Mann, M., and Wilm, M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66, 4390-4399
2. Tanner, S., Shu, H., Frank, A., Wang, L., Zandi, E., Mumby, M., Pevzner, P., and Bafna, V. (2005) InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 77, 4626-4639
3. Shilov, I., Seymour, S., Patel, A., Loboda, A., Tang, W., Keating, S., Hunter, C., Nuwaysir, L., and Schaeffer, D. (2007) The Paragon Algorithm: a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol. Cell. Proteomics 6, 1638-1655
4. Frank, A., Tanner, S., Bafna, V., and Pevzner, P. (2005) Peptide sequence tags for fast database search in mass-spectrometry. J. Proteome Res. 4, 1287-1295
5. 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
6. Taylor, J., and Johnson, R. (1997) Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom. 11, 1067-1075
7. Alves, G., and Yu, Y. (2005) Robust accurate identification of peptides (RAld): deciphering MS2 data using a structured library search with de novo based statistics. Bioinformatics 21, 3726-3732
8. Jaffe, J., Berg, H., and Church, G. (2004) Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4, 59-77
9. Kalume, D., Pen, S., Reddy, R., Zhong, J., Okulate, M., Kumar, N., and Pandey, A. (2005) Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics 6, 128-138
10. Wang, R., Prince, J., and Marcotte, E. (2005) Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res. 15, 1118-1126
11. Fermin, D., Allen, B., Blackwell, T., Menon, R., Adamski, M., Xu, Y., Ulintz, P., Omenn, G., and States, D. (2006) Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol. 7, R35
12. Savidor, A., Donahoo, R., Hurtado-Gonzales, O., VerBerkmoes, N., Shah, M., Lamour, K., and McDonald, W. (2006) Expressed peptide tags: an additional layer of data for genome annotation. J. Proteome Res. 5, 3048-3058
13. Tanner, S., Shen, Z., Ng, J., Florea, L., Guigo, R., Briggs, S., and Bafna, V. (2007) Improving gene annotation using peptide mass spectrometry. Genome Res. 17, 231-239
14. Gupta, N., Tanner, S., Jaitly, N., Adkins, J., Lipton, M., Edwards, R., Romine, M., Osterman, A., Bafna, V., Smith, R., and Pevzner, P. (2007) Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation, Genome Res. 17, 1362-1377
15. Gupta, N., Benhamida, J., Bhargava, D., Goodman, E., Kain, I., Nguyen, N., Ollikainen, N., Rodriguez, J., Wang, J., Lipton, M., Romine, M., Bafna, V., Smith, R., and Pevzner, P. (2008) Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res. 18, 1133-1142
16. Siepel, A., Diekhans, M., Brejová, B., Langton, L., Stevens, M., Comstock, C., Davis, C., Ewing, B., Oommen, S., Lau, C., Yu, H., Li, J., Roe, B., Green, P., Gerhard, D., Temple, G., Haussler, D., and Brent, M. (2007) Targeted discovery of novel human exons by comparative genomics. Genome Res. 17, 1763-1773
17. Stark, A., Lin, M., Kheradpour, P., Pedersen, J., Parts, L., Carison, J., Crosby, M., Rasmussen, M., Roy, S., Deoras, A., Ruby, J., Brennecke, J., Hodges, E., Hinrichs, A., Caspi, A., Paten, B., Park, S., Han, M., Maeder, M., Polansky, B., Robson, B., Aerts, S., van Helden, J., Hassan, B., Gilbert, D., Eastman, D., Rice, M., Weir, M., Hahn, M., Park, Y., Dewey, C., Pachter, L., Kent, W., Haussler, D., Lai, E., Bartel, D., Hannon, G., Kaufman, T., Eisen, M., Clark, A., Smith, D., Celniker, S., Gelbart, W., and Kellis, M. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219-232
18. Ng, J., and Pevzner, P. (2008) Algorithm for identification of fusion proteins via mass spectrometry. J. Proteome Res. 7, 89-95
19. Taylor, J., and Johnson, R. (2001) Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal. Chem. 73, 2594-2604
20. Dancik, V., Addona, T., Clauser, K., Vath, J., and Pevzner, P. (1999) De novo protein sequencing via tandem mass-spectrometry. J. Comp. Biol. 6, 327-341
21. Frank, A., and Pevzner, P. (2005) PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem. 77, 964-973
22. 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
23. Bern, M., and Goldberg, D. (2006) De novo analysis of peptide tandem mass spectra by spectral graph partitioning. J. Comput. Biol. 13, 364-378
24. Fischer, B., Roth, V., Roos, F., Grossmann, J., Baginsky, S., Widmayer, P., Gruissem, W., and Buhmann, J. (2005) NovoHMM: a hidden Markov model for de novo peptide sequencing. Anal. Chem. 77, 7265-7273
25. Grossmann, J., Roos, F., Cieliebak, M., Liptak, Z., Mathis, L., Muller, M., Gruissem, W., and Baginsky, S. (2005) AUDENS: a tool for automated peptide de novo sequencing. J. Proteome Res. 4, 1768-1774
26. Mo, L., Dutta, D., Wan, Y., and Chen, T. (2007) MSNovo: a dynamic programming algorithm for de novo peptide sequencing via tandem mass spectrometry. Anal. Chem. 79, 4870-4878
27. Dimaggio, P., Jr., and Floudas, C. (2007) De novo peptide identification via tandem mass spectrometry and integer linear optimization. Anal. Chem. 79, 1433-1446
28. Chen, T., Kao, M., Tepel, M., Rush, J., and Church, G. (2001) A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 8, 325-337
29. Bafna, V., and Edwards, N. (2003) On de novo interpretation of tandem mass spectra for peptide identification, in Proceedings of the Seventh Annual International Conference on Computational Molecular Biology, Berlin, April 10-13, 2003, pp. 9-18, Association for Computing Machinery, New York
30. Chong, K., Ning, K., Leong, H., and Pevzner, P. (2006) Modeling and characterization of multi-charge mass spectra for peptide sequencing. J. Bioinform. Comput. Biol. 4, 1329-1352
31. Craig, R., and Beavis, R. (2004) TANDEM: matching proteins with tandem mass-spectra. Bioinformatics 20, 1466-1467
32. Creasy, D., and Cottrell, J. (2002) Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics 2, 1426-1434
33. Eng, J., McCormack, A., and Yates, J. (1994) 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
34. Clauser, K., Baker, P., and Burlingame, A. (1999) Role of accurate mass measurement (± 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871-2882
35. Geer, L., Markey, S., Kowalak, J., Wagner, L., Xu, M., Maynard, D., Yang, X., Shi, W., and Bryant, S. (2004) Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964
36. Cao, X., and Nesvizhskii, A. (2008) Improved sequence tag identification method for peptide identification in tandem mass spectrometry. J. Proteome Res. 7, 4422-4434
37. Gusfield, D. (1997) Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, pp. 87-123, Cambridge University Press, Cambridge, UK
38. Kim, S., Gupta, N., and Pevzner, P. (2008) Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res. 7, 3354-3363
39. Havilio, M., Haddad, Y., and Smilansky, Z. (2003) Intensity-based statistical scorer for tandem mass spectrometry. Anal. Chem. 75, 435-444
40. 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
41. Bandeira, N., Olsen, J., Mann, M., and Pevzner, P. (2008) Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics 24, i416-i423
42. Bartels, C. (1990) Fast algorithm for peptide sequencing by mass spectroscopy. J. Proteome Res. 19, 363-368
43. 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, Suppl. 2, ii113-ii121
44. Matthiesen, R., Trelle, M., Højrup, P., Bunkenborg, J., and Jensen, O. (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
45. Ma, B., Zhang, K., and Liang, C. (2005) An effective algorithm for peptide de novo sequencing from MS/MS spectra. J. Comput. Syst. Sci. 70, 418-430
46. Frank, A., Savitski, M., Nielsen, M., Zubarev, R., and Pevzner, P. (2007) De novo peptide sequencing and identification with precision mass spectrometry. J. Proteome Res. 6, 114-123
47. Zhang, Z. (2004) De novo peptide sequencing based on a divide-and-conquer algorithm and peptide tandem spectrum simulation. Anal. Chem. 76, 6374-6383
48. Bafna, V., and Edwards, N. (2001) Scope: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics 17, Suppl. 1, 13-21
49. Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410
50. Jaffe, J., Stange-Thomann, N., Smith, C., DeCaprio, D., Fisher, S., Butler, J., Calvo, S., Elkins, T., FitzGerald, M., Hafez, N., Kodira, C., Major, J., Wang, S., Wilkinson, J., Nicol, R., Nusbaum, C., Birren, B., Berg, H., and Church, G. (2004) The complete genome and proteome of Mycoplasma mobile. Genome Res. 14, 1447-1461
51. Edwards, N. (2007) Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Mol. Syst. Biol. 3, 102-108
52. Payne, S., Yau, M., Smolka, M., Tanner, S., Zhou, H., and Bafna, V. (2008) Phosphorylation specific ms/ms scoring for rapid and accurate phospho-proteome analysis. J. Proteome Res. 7, 3373-3381
53. Frank, A., Bandeira, N., Shen, Z., Tanner, S., Briggs, S., Smith, R., and Pevzner, P. (2008) Clustering millions of tandem mass spectra. J. Proteome Res. 7, 113-122