Algorithm development of de novo peptide sequencing via tandem mass spectrometry

Progress in Biochemistry and Biophysics

Volumn 37, Issue 12, 2010, Pages 1278-1288

  Sun, Han Chang ^a   Zhang, Ji Yang ^a   Liu, Hui ^a   Zhang, Wei ^a   Xu, Chang Ming ^a   Ma, Hai Bin ^a   Zhu, Yun Ping ^b   Xie, Hong Wei ^a  

^a NATIONAL UNIVERSITY OF DEFENSE TECHNOLOGY   (China)

^b BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

Author keywords

Algorithm development; Computational proteomics; De novo sequencing; Peptide; Tandem mass spectrometry

Indexed keywords

EID: 79951892439     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: 10.3724/SP.J.1206.2010.00226     Document Type: Review

References (69)

1. James P. Protein identification in the post-genome era: the rapid rise of proteomics. Q Rev Biophys, 1997, 30(4): 279-331 (Pubitemid 28260612)
2. Anderson N L, Anderson N G. Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis, 1998, 19(11): 1853-1861 (Pubitemid 28392230)
3. Blackstock W P, Weir M P. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol, 1999, 17(3): 121-127 (Pubitemid 29348464)
4. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature, 2003, 422(6928): 198-207 (Pubitemid 36362757)
5. Binz P A, Hochstrasser D F, Appel R D. Mass spectrometry-based proteomics: current status and potential use in clinical chemistry. Clin Chem Lab Med, 2003, 41(12): 1540-1551 (Pubitemid 38055005)
6. Pusch W, Flocco M T, Leung S M, et al. Mass spectrometry-based clinical proteomics. Pharmacogenomics, 2003, 4(4): 463-476 (Pubitemid 36857180)
7. Kolialexi A, Mavrou A, Spyrou G, et al. Mass spectrometry-based proteomics in reproductive medicine. Mass Spectrom Rev, 2008, 27(6): 624-634
8. Frobel J, Lehr S, Haas R, et al. Mass spectrometry-based proteomics and its potential use in haematological research. Arch Physiol Biochem, 2009, 115(5): 286-297
9. Domon B, Aebersold R. Mass spectrometry and protein analysis. Science, 2006, 312(5771): 212-217
10. Nesvizhskii A I, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods, 2007, 4(10): 787-797 (Pubitemid 350055575)
11. Marcotte E M. How do shotgun proteomics algorithms identify proteins?. Nat Biotech, 2007, 25(7): 755-757 (Pubitemid 47053867)
12. Steen H, Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol, 2004, 5(9): 699-711 (Pubitemid 39208180)
13. Sakurai T, Matsuo T, Matsuda H, et al. PAAS 3: A computer program to determine probable sequence of peptides from mass spectrometric data. Biological Mass Spectrometry, 1984, 11 (8): 396-399
14. Hamm C W, Wilson W E, Harvan D J. Peptide sequencing program. Comput Appl Biosci, 1986, 2(2): 115-118 (Pubitemid 16022896)
15. Ishikawa K, Niwa Y. Computer-aided peptide sequencing by fast atom bombardment mass spectrometry. Biological Mass Spectrometry, 1986, 13(7): 373-380
16. Siegel M M, Bauman N. An efficient algorithm for sequencing peptides using fast atom bombardment mass spectral data. Biological Mass Spectrometry, 1988, 15(6): 333-343
17. Johnson R S, Biemann K. Computer program (SEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides. Biomed Environ Mass Spectrom, 1989, 18(11): 945-957 (Pubitemid 19268410)
18. Zidarov D, Thibault P, Evans M J, et al. Determination of the primary structure of peptides using fast atom bombardment mass spectrometry. Biological Mass Spectrometry, 1990, 19(1): 13-26 (Pubitemid 20076146)
19. 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(8): 1041-1049 (Pubitemid 44094120)
20. Lu B, Chen T. Algorithms for de novo peptide sequencing using tandem mass spectrometry. Drug Discovery Today: BIOSILICO, 2004, 2(2): 85-90 (Pubitemid 40136865)
21. Xu C, Ma B. Software for computational peptide identification from MS-MS data. Drug Discov Today, 2006, 11(13-14): 595-600
22. Bartels C. Fast algorithm for peptide sequencing by mass spectroscopy. Biomedical and Environmental Mass Spectrometry, 1990, 19(6): 363-368 (Pubitemid 20326751)
23. Fernandez-de-Cossio J, Gonzalez J, Besada V. A computer program to aid the sequencing of peptides in collision-activated decomposition experiments. Comput Appl Biosci, 1995, 11(4): 427-434
24. Fernandez-de-Cossio J, Gonzalez J, Betancourt L, et al. Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by 'SeqMS', a software aid for de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom, 1998, 12(23): 1867-1878 (Pubitemid 28548079)
25. Taylor J A, Johnson R S. Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom, 1997, 11(9): 1067-1075 (Pubitemid 27269545)
26. Taylor J A, Johnson R S. Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem, 2001, 73(11): 2594-2604 (Pubitemid 32880663)
27. Johnson R S, Taylor J A. Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry. Mol Biotechnol, 2002, 22(3): 301-315 (Pubitemid 35252826)
28. Dancik V, Addona T A, Clauser K R, et al. De novo peptide sequencing via tandem mass spectrometry. J Comput Biol, 1999, 6(3-4): 327-342
29. Chen T, Kao M Y, Tepel M, et al. A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J Comput Biol, 2001, 8(3): 325-337 (Pubitemid 32911660)
30. Havilio M, Haddad Y, Smilansky Z. Intensity-based statistical scorer for tandem mass spectrometry. Anal Chem, 2003, 75 (3): 435-444 (Pubitemid 36176713)
31. Frank A, Pevzner P. PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem, 2005, 77(4): 964-973 (Pubitemid 40261761)
32. Grossmann J, Roos F F, Cieliebak M, et al. AUDENS: a tool for automated peptide de novo sequencing. J Proteome Res, 2005, 4(5): 1768-1774 (Pubitemid 41464805)
33. Mo L, Dutta D, Wan Y, et al. MSNovo: a dynamic programming algorithm for de novo peptide sequencing via tandem mass spectrometry. Anal Chem, 2007, 79(13): 4870-4878 (Pubitemid 47051439)
34. DiMaggio P A, Jr, Floudas C A. De novo peptide identification via tandem mass spectrometry and integer linear optimization. Anal Chem, 2007, 79(4): 1433-1446
35. DiMaggio P A, Jr, Floudas C A, Lu B, et al. 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, 2008, 7(4): 1584-1593
36. Chi H, Sun R X, Yang B, et al. pNovo: de novo peptide sequencing and identification using HCD spectra. J Proteome Res, 2010, 9(5): 2713-2724
37. Bern M, Goldberg D. De novo analysis of peptide tandem mass spectra by spectral graph partitioning. J Comput Biol, 2006, 13(2): 364-378
38. Yan B, Qu Y, Mao F, et al. PRIME: A mass spectrum data mining tool for de novo sequencing and PTMs identification. J Comp Sci Tech, 2005, 20(4): 483-490 (Pubitemid 43257722)
39. Yan B, Pan C, Olman V N, et al. A graph-theoretic approach for the separation of b and y ions in tandem mass spectra. Bioinformatics, 2005, 21(5): 563-574 (Pubitemid 40424780)
40. Lu B, Chen T. A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry. J Comput Biol, 2003, 10(1): 1-12 (Pubitemid 36315619)
41. Liu C, Song Y, Yan B, et al. Fast de novo peptide sequencing and spectral alignment via tree decomposition//Pac Symp Biocomput, Hawaii, 2006: 255-266
42. Ning K, Leong H W. Algorithm for peptide sequencing by tandem mass spectrometry based on better preprocessing and antisymmetric computational model. Comput Syst Bioinformatics Conf, 2007, 6: 19-30
43. Ma B, Zhang K, Hendrie C, et al. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom, 2003, 17(20): 2337-2342 (Pubitemid 37243319)
44. Ma B, Zhang K, Liang C. An effective algorithm for peptide de novo sequencing from MS/MS spectra. J Comp Sys Sci, 2005, 70(3): 418-430 (Pubitemid 40391418)
45. Alves G, Yu Y K. Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. Bioinformatics, 2005, 21(19): 3726-3732 (Pubitemid 41535520)
46. Fischer B, Roth V, Roos F, et al. NovoHMM: a hidden Markov model for de novo peptide sequencing. Anal Chem, 2005, 77(22): 7265-7273 (Pubitemid 41681392)
47. Spengler B. De novo sequencing, peptide composition analysis, and composition-based sequencing: a new strategy employing accurate mass determination by fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom, 2004, 15(5): 703-714 (Pubitemid 38581097)
48. Zhang Z. De novo peptide sequencing based on a divide-and- conquer algorithm and peptide tandem spectrum simulation. Anal Chem, 2004, 76(21): 6374-6383 (Pubitemid 39458471)
49. Zhang Z. Prediction of low-energy collision-induced dissociation spectra of peptides. Anal Chem, 2004, 76(14): 3908-3922 (Pubitemid 38943659)
50. Zhang Z. Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal Chem, 2005, 77(19): 6364-6373 (Pubitemid 41436975)
51. Bruni R, Gianfranceschi G, Koch G. On peptide de novo sequencing: a new approach. J Pept Sci, 2005, 11(4): 225-234 (Pubitemid 40542354)
52. Zhang Z, McElvain J S. De novo peptide sequencing by two-dimensional fragment correlation mass spectrometry. Anal Chem, 2000, 72(11): 2337-2350 (Pubitemid 30395630)
53. Demine R, Walden P. Sequit: software for de novo peptide sequencing by matrix-assisted laser desorption/ionization postsource decay mass spectrometry. Rapid Commun Mass Spectrom, 2004, 18(8): 907-913 (Pubitemid 38520257)
54. Heredia-Langner A, Cannon W R, Jarman K D, et al. Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data. Bioinformatics, 2004, 20(14): 2296-2304 (Pubitemid 39345135)
55. Kanazawa M, Anyoji H, Ogiwara A, et al. De novo peptide sequencing using ion peak intensity and amino acid cleavage intensity ratio. Bioinformatics, 2007, 23(9): 1068-1072 (Pubitemid 47050557)
56. Pevtsov S, Fedulova I, Mirzaei H, et al. Performance evaluation of existing de novo sequencing algorithms. J Proteome Res, 2006, 5(11): 3018-3028 (Pubitemid 44754676)
57. Pitzer E, Masselot A, Colinge J. Assessing peptide de novo sequencing algorithms performance on large and diverse data sets. Proteomics, 2007, 7(17): 3051-3054 (Pubitemid 47477949)
58. Frank A M, Savitski M M, Nielsen M L, et al. De novo peptide sequencing and identification with precision mass spectrometry. J Proteome Res, 2007, 6(1): 114-123 (Pubitemid 46173663)
59. Waridel P, Frank A, Thomas H, et al. Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing. Proteomics, 2007, 7(14): 2318-2329 (Pubitemid 47121523)
60. Perkins D, Pappin D, Creasy D, et al. Probability-based protein identification by searching sequence database using mass spectrometry data. Electrophoresis, 1999, 20(18): 3551-3567 (Pubitemid 30007252)
61. Bandeira N, Pham V, Pevzner P, et al. Automated de novo protein sequencing of monoclonal antibodies. Nat Biotechnol, 2008, 26(12): 1336-1338
62. Ng J, Bandeira N, Liu W T, et al. Dereplication and de novo sequencing of nonribosomal peptides. Nat Methods, 2009, 6 (8): 596-599
63. Kim H J, Lee D Y, Lee D H, et al. Strategic proteome analysis of Candida magnoliae with an unsequenced genome. Proteomics, 2004, 4(11): 3588-3599
64. Lilla S, Pereira R, Hyslop S, et al. Purification and initial characterization of a novel protein with factor Xa activity from Lonomia obliqua caterpillar spicules. J Mass Spectrom, 2005, 40(3): 405-412 (Pubitemid 40392878)
65. Kim S, Gupta N, Bandeira N, et al. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics, 2009, 8(1): 53-69
66. Kim S, Bandeira N, Pevzner P A. Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification. Mol Cell Proteomics, 2009, 8(6): 1391-1400
67. Bertsch A, Leinenbach A, Pervukhin A, et al. De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis, 2009, 30(21): 3736-3747
68. Datta R, Bern M. Spectrum fusion: using multiple mass spectra for de novo Peptide sequencing. J Comput Biol, 2009, 16 (8): 1169-1182
69. Bandeira N, Olsen J V, Mann J V, et al. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics, 2008, 24(13): i416-i423