De novo peptide sequencing and identification with precision mass spectrometry

Journal of Proteome Research

Volumn 6, Issue 1, 2007, Pages 114-123

  Frank, Ari M ^a   Savitski, Mikhail M ^b   Nielsen, Michael L ^b   Zubarev, Roman A ^b   Pevzner, Pavel A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Database search; De novo; Filtration; FT ICR; FTMS; LTQ FT; MS MS; Pattern matching; Precision MS

Indexed keywords

HOMEOMETRIC PEPTIDE; PEPTIDE DERIVATIVE; PEPTIDE FRAGMENT; UNCLASSIFIED DRUG;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; DATA BASE; INFRARED SPECTROSCOPY; INTERMETHOD COMPARISON; MASS SPECTROMETRY; PEPTIDE ANALYSIS; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ALGORITHMS; ALTERNATIVE SPLICING; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; DATABASES, PROTEIN; FOURIER ANALYSIS; GENOME, HUMAN; GENOMICS; HUMANS; MASS SPECTROMETRY; NEOPLASM PROTEINS; PEPTIDES; PROBABILITY; SEQUENCE ANALYSIS, PROTEIN; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

EID: 33846600820     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr060271u     Document Type: Article

References (41)

1. Siuzdak, G. The Expanding Role of Mass Spectrometry in Biotechnology, MCC Press: San Diego, CA, 2003.
2. Marshall, A. G.; Hendrickson, C. L. Fourier transform ion cyclotron resonance detection: Principles and experimental configurations. Int. J. Mass Spectrom. 2002, 215, 59-75.
3. Olsen, J. V.; de Godoy, L. M. F.; Li, G.; Macek, B.; Mortensen, P.; Pesch, R.; Makarov, A.; Lange, O.; Horning, S.; Mann, M. Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 2005, 4, 2010-2021.
4. Eng, J. K.; McCormack, A. L.; Yates, 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. 1994, 5, 976-989.
5. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
6. Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
7. Tanner, S.; Shu, H.; Frank, A.; Mumby, M.; Pevzner, P.; Bafna, V. Inspect: Fast and accurate identification of post-translationally modified peptides from tandem mass spectra. Anal. Chem. 2005, 77, 4626-4639.
8. Taylor, J. A.; Johnson, R. S. Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom. 1997, 11, 1067-1075.
9. Dancík, V.; Addona, T. A.; Clauser, K. R.; Vath, J. E.; Pevzner, P. A. De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 1999, 6, 327-342.
10. Zhang, Z.; McElvain, J. S. De novo peptide sequencing by two-dimensional fragment correlation mass spectrometry. Anal. Chem. 2000, 72, 2337-2350.
11. Taylor, J. A.; Johnson, R. S. Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal. Chem. 2001, 73, 2594-2604.
12. Chen, T.; Kao, M. Y.; Tepel, M.; Rush, J.; Church, G. M. A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 2001, 8, 325-337.
13. Lubeck, O.; Sewell, C.; Gu, S.; Chen, X.; Cai, D. New computational approaches for de novo peptide sequencing from MS/MS experiments. IEEE Proc. Challenges Biomedical Inform. 2002, 90, 1868-1874.
14. Bafha, V.; Edwards, N. On de-novo interpretation of tandem mass spectra for peptide identification. In Proceedings of the Seventh Annual International Conference on Computational Molecular Biology, ACM Press: New York, 2003; pp 9-18.
15. Ma, B.; Zhang, K.; Hendrie, C.; Liang, C.; Li, M.; Doherty-Kirby, A.; Lajoie, G. PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2003, 17, 2337-2342.
16. Frank, A.; Pevzner, P. Pepnovo: De novo peptide sequencing via probabilistic network modeling. Anal. Chem. 2005, 77, 964-973.
17. Bern, M. W.; Goldberg, D. EigenMS: De novo analysis of peptide tandem mass spectra by spectral graph partitioning. In Proceedings of the Ninth Annual International Conference on Research in Computational Molecular Bilogy (RECOMB 2005); Springer: Heidelberg, Germany, 2005; pp 357-372.
18. Fischer, B.; Roth, V.; Roos, F.; Grossmann, J.; Baginsky, S.; Widmayer, P.; Gruissem, W.; Buhmann, J. M. NovoHMM: A Hidden Markov Model for de novo peptide sequencing. Anal. Chem. 2005, 77, 7265-7273.
19. Savitski, M. M.; Nielsen, M. L.; Kjeldsen, F.; Zubarev, R. A. Proteomics-grade de novo sequencing approach. J. Proteome Res. 2005, 4, 2348-2354.
20. Mann, M.; Wilm, M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 1994, 66, 4390-4399.
21. Mørtz, E.; O'Connor, P. B.; Roepstorff, P.; Kelleher, N. L.; Wood, T. D.; McLafferty, F. W.; Mann, M. Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence data bases. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 8264-8267.
22. Clauser, K. R.; Baker, P. R.; Burlingame, A. L. Role of accurate mass measurement (+/- 10 ppm) in protein identication strategies employing ms or ms/ms and database searching. Anal. Chem. 1999, 71, 2871-2882.
23. Tabb, D. L.; Saraf, A.; Yates, J. R. GutenTag: High-throughput sequence tagging via an empirically derived fragmentation model. Anal. Chem. 2003, 75, 6415-6421.
24. Frank, A.; Tanner, S. W.; Bafna, V.; Pevzner, P. A. Peptide sequence tags for fast database search in mass-spectrometry. J. Proteome Res. 2005, 4, 1287-1295.
25. Shevchenko, A.; Loboda, A.; Sunyaev, S.; Shevchenko, A.; Bork, P.; Ens, W.; Standing, K. G. Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of flight mass spectrometry and BLAST homology searching. Anal. Chem. 2001, 73, 1917-1926.
26. Searle, B. C.; Dasari, S.; Turner, M.; Reddy, A. P.; Choi, D.; Wilmarth, P. A.; McCormack, A. L.; David, L. L.; Nagalla, S. R. High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for ms/ms de novo sequencing results. Anal. Chem. 2004, 76, 2220-2230.
27. Han, Y.; Ma, B.; Zhang, K. SPIDER: Software for protein identification from sequence tags with de novo sequencing error. J. Bioinform. Comput. Biol. 2005, 3, 697-716.
28. Horn, D. M.; Zubarev, R. A.; McLafferty, F. W. Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 10313-10317.
29. Spengler, B. De novo sequencing, peptide composition analysis, and compositionbased sequencing: a new strategy employing accurate mass determination by Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 2004, 15, 703-714.
30. Olson, M. T.; Epstein, J. A.; Yergey, A. L. De novo peptide sequencing using exhaustive enumeration of peptide composition. J. Am. Soc. Mass Spectrom. 2006, 17, 1041-1049.
31. Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A. New data base-independent, sequence tag-based scoring of peptide MS/MS data validates mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of ms/ms techniques. Mol. Cell. Proteomics 2005, 4, 1180-1188.
32. Tanner, S.; Shen, Z.; Ng, J.; Florea, L.; Guigó, R.; Briggs, S. P.; Bafna, V. Improving gene annotation using peptide mass spectrometry. Manuscript in preparation.
33. Budnik, B. A.; Nielsen, M. L.; Olsen, J. V.; Haselmann, K. F.; Hörth, P.; Haehnel, W.; Zubarev, R. A. Can relative cleavage frequencies in peptides provide additional sequence information? Int. J. Mass Spectrom. 2002, 219, 283-294.
34. Bartels, C. Fast algorithm for peptide sequencing by mass spectroscopy. Biomed. Environ. Mass Spectrom. 1990, 19, 363-368.
35. Marshall, A. G.; Verdun, F. R. Fourier transforms in NMR, optical, and mass spectrometry: A user's handbook; Elsevier: New York, 1990.
36. Tabb, D. L.; Smith, L. L.; Breci, L. A.; Wysocki, V. H.; Lin, D.; Yates, J. R. Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal. Chem. 2003, 75, 1155-1163.
37. Havilio, M.; Haddad, Y.; Smilansky, Z. Intensity-based statistical scorer for tandem mass spectrometry. Anal. Chem. 2003, 75, 435-444.
38. Huang, Y.; Triscari, J. M.; Tseng, G. C.; Pasa-Tolic, L.; Lipton, M. S.; Smith, R. D.; Wysocki, V. H. Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal. Chem. 2005, 77, 5800-5813.
39. Creasy, D. M.; Cottrell, J. S. Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics 2002, 2, 1426-1434.
40. Bandeira, N.; Tsur, D.; Frank, A.; Pevzner, P. A. A new approach to protein identification. In Proceedings of the 10th Annual International Conference on Computational Molecular Biology, volume 3909 of Lecture Notes in Computer Science; Springer: Hidelberg, Germany; pp 363-378.
41. Shevchenko, A.; Sunyaev, S.; Liska, A.; Bork, P.; Shevchenko, A. Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes. Methods Mol. Biol. 2003, 211, 221-234.