NovoHCD: De novo peptide sequencing from HCD spectra

IEEE Transactions on Nanobioscience

Volumn 13, Issue 2, 2014, Pages 65-72

  Yan, Yan ^a   Kusalik, Anthony J ^a   Wu, Fang Xiang ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

Amino acid combination; HCD spectra; MS MS de novo peptide sequencing; multi edge spectrum graph; peptide tags

Indexed keywords

AMINO ACIDS; GRAPH THEORY; MASS SPECTROMETRY;

COLLISIONAL DISSOCIATION; DE NOVO PEPTIDE SEQUENCING; GRAPH MODEL; MASS SPECTROMETRY DATA; MULTI-EDGE SPECTRUM GRAPH; PEPTIDE IDENTIFICATION; PEPTIDE TAGS; TANDEM MASS SPECTRA;

PEPTIDES;

PEPTIDE;

ALGORITHM; CHEMISTRY; PROCEDURES; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY; THEORETICAL MODEL;

ALGORITHMS; MODELS, THEORETICAL; PEPTIDES; SEQUENCE ANALYSIS, PROTEIN; TANDEM MASS SPECTROMETRY;

EID: 84902013206     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2014.2316424     Document Type: Article

References (27)

1. G. Johoson and K. Biemann, "Computer program (DEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides," Biomed. Environ. Mass Spectrom., vol. 18, pp. 945-957, 1989. (Pubitemid 19268410)
2. L. McHugh and J. Arthur, "Computational methods for protein identification from mass spectrometry data," PLoS Comput. Biol., vol. 4, no. 2, pp. 1-12, 2008.
3. V. Wysockia et al., "Mass spectrometry of peptides and proteins," Methods, vol. 35, pp. 211-222, 2005.
4. F. McLafferty and F. Turecek, Interpretation of Mass Spectra, 4th ed. Sausolito, CA, USA: United Science Books, 1993.
5. J. Pitt, "Principles and aplications of liquid chromatographymass spectrometry in clinical biochemistry," Clin. Biochem. Rev., vol. 30, pp. 19-34, 2009.
6. A. Marshall, C. Hendrickson, and G. Jackson, "Fourier transform ion cyclotron resonance mass spectrometry: a primer," Mass Spectrom. Rev., vol. 17, pp. 1-35, 1998. (Pubitemid 128629493)
7. A. Michalski et al., "A systematic investigation into the nature of tryptic HCD spectra," J. Proteome Res., vol. 11, no. 11, pp. 5479-5491, 2012.
8. L. He and B. Ma, "ADEPTS: advance peptide de novo sequencing with a pair of tandem mass spectra," J. Bioinformat. Comput. Biol., vol. 8, pp. 981-994, 2010.
9. B. Lu and T. Chen, "Algorithms for de novo peptide sequencing using tandem mass spectrometry," BIOSILICO, vol. 2, pp. 85-90, 2004. (Pubitemid 40136865)
10. A. Frank and P. A. Pevzner, "Pepnovo: de novo peptide sequencing via probabilistic network modeling," Anal. Chem., vol. 77, pp. 964-973, 2005. (Pubitemid 40261761)
11. C. Pan et al., "A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry," BMC Bioinformat., vol. 11, no. 1, p. 118.
12. B. Ma et al., "PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry," Rapid Commun. Mass Spectrom., vol. 17, pp. 2337-2342, 2003. (Pubitemid 37243319)
13. Y. Yan, S. Zhang, and F. -X. Wu, "Applications of graph theory in protein structure identification," Proteome Sci., vol. 9, no. Suppl. 1, p. S17, 2011.
14. H. Chi et al., "Pnovo: De novo peptide sequencing and identification using HCD spectra," J. Proteome Res., vol. 9, no. 5, pp. 2713-2724, 2010.
15. D. L. Tabb et al., "Directag: Accurate sequence tags from peptide ms/ms through statistical scoring," J. Proteome Res., vol. 7, no. 9, pp. 3838-3846, 2008.
16. V. Sridhara et al., "Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge," Proteome Sci., vol. 10, no. 1, p. 8, 2012.
17. Y. Shen et al., "Effectiveness of CID, HCD, andETDwith ft ms/ms for degradomic-peptidomic analysis: Comparison of peptide identification methods," J. Proteome Res., vol. 10, no. 9, pp. 3929-3943, 2011.
18. H. Chi et al., "Pnovo+: de novo peptide sequencing using complementary HCD and ETD tandem mass spectra," J. Proteome Res., vol. 12, no. 2, pp. 615-625, 2013.
19. C. K. Frese et al., "Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-orbitrap velos," J. Proteome Res., vol. 10, no. 5, pp. 2377-2388, 2011.
20. A. V. Nefedov, I. Mitra, A. R. Brasier, and R. G. Sadygov, "Examining troughs in the mass distribution of all theoretically possible tryptic peptides," J. Proteome Res., vol. 10, no. 9, pp. 4150-4157, 2011.
21. T. A. Hansen, F. Kryuchkov, and F. Kjeldsen, "Reduction in database search space by utilization of amino acid composition information from electron transfer dissociation and higher-energy collisional dissociation mass spectra," Anal. Chem., vol. 84, no. 15, pp. 6638-6645, 2012.
22. Y. Yan, A. J. Kusalik, and F. -X. Wu, "A multi-edge graph based de novo peptide sequencing method for HCD spectra," in Proc. IEEE Int. Conf. Bioinformat. Biomed. (BIBM), Dec. 2013, pp. 176-181.
23. B. Ma, K. Zhang, and C. Liang, "An effective algorithm for peptide de novo sequencing from ms/ms spectra," J. Comput. Syst. Sci., vol. 70, no. 3, pp. 418-430, 2005. (Pubitemid 40391418)
24. J. Ding, J. Shi, G. Poirier, and F. -X. Wu, "A novel approach to denoising ion trap tandem mass spectra," Proteome Sci., vol. 7, no. 1, p. 9.
25. A. Goloborodko, M. Gorshkov, D. Good, and R. Zubarev, "Sequence scrambling in shotgun proteomics is negligible," J. Amer. Soc. Mass Spectrometry, vol. 22, no. 7, pp. 1121-1124, 2011.
26. C. K. Frese et al., "Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-orbitrap velos," J. Proteome Res., vol. 10, no. 5, pp. 2377-2388, 2011.
27. Matrix science 2013 [Online]. Available: http://www.matrixscience. com/