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A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry
Abstract
Tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged molecules of prefix and suffix peptide subsequences and then measures mass/charge ratios of these ions. The de novo peptide sequencing problem is to reconstruct the peptide sequence from a given tandem mass spectral data of k ions. By implicitly transforming the spectral data into an NC-spectrum graph G (V, E) where /V/ = 2k + 2, we can solve this problem in O(/V//E/) time and O(/V/2) space using dynamic programming. For an ideal noise-free spectrum with only b- and y-ions, we improve the algorithm to O(/V/ + /E/) time and O(/V/) space. Our approach can be further used to discover a modified amino acid in O(/V//E/) time. The algorithms have been implemented and tested on experimental data.
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Cited by
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
Ma, B., Zhang, K., Hendrie, C., Liang, C., Li, M., Doherty‐Kirby, A., & Lajoie, G. (2003) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.1196 · Cited by 1,379
Machine learning in bioinformatics
Larrañaga, P., Calvo, B., Santana, R., Bielza, C., Galdiano, J., Inza, I., Lozano, J. A., Armañanzas, R., Santafé, G., Pérez, A., et al. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbk007 · Cited by 867
InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra
Tanner, S., Shu, H., Frank, A., Wang, L.-C., Zandi, E., Mumby, M., Pevzner, P. A., & Bafna, V. (2005) · Analytical Chemistry · doi:10.1021/ac050102d · Cited by 567
ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity
Xu, T., Park, S. K., Venable, J. D., Wohlschlegel, J. A., Diedrich, J. K., Cociorva, D., Lu, B., Liao, L., Hewel, J., Han, X., et al. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.07.001 · Cited by 511
Metadata
- Authors
- Chen, T., Kao, M.-Y., Tepel, M., Rush, J., & Church, G. M.
- Venue
- Journal of Computational Biology
- Publisher
- SAGE Publications
- Published
- 2001-06
- Volume
- 8
- Issue
- 3
- Pages
- 325-337
- ISSN
- 1066-5277 (ISSN-L)
- 1557-8666
- OpenAlex
- W3136323740
- Cited by
- 248
- References
- 0
- FWCI
- 5.42
- Type
- journal article
- Language
- en
- Open access
- closed
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- Chen, T., Kao, M.-Y., Tepel, M., Rush, J., & Church, G. M. (2001). A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry. Journal of Computational Biology. https://doi.org/10.1089/10665270152530872
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