De Novo Interpretation of Tandem Mass Spectra
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- Abstract
- Table of Contents
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Abstract
De novo sequencing is an effective method for identifying unknown peptide sequences from their tandem mass spectra. This unit briefly introduces how this can be done manually. A protocol for using the PEAKS online software for automated de novo sequencing is described. Finally, we show how to use the PEAKS scores to validate the de novo sequencing results. Curr. Protoc. Bioinform. 25:13.10.1?13.10.8. © 2009 by John Wiley & Sons, Inc.
Keywords: de novo sequencing; tandem mass spectrometry; protein identification; peptide sequencing; PEAKS software
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Basic Principles
- Basic Protocol 1: Auto De Novo Sequencing with PEAKS Software
- Alternate Protocol 1: De Novo Sequencing with PEAKS Studio or Client
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
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PDF or HTML at Wiley Online LibraryFigures
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Figure 13.10.1 The spectrum contains clear y‐ion ladders, which can be used to derive the peptide sequence. View Image -
Figure 13.10.2 The input page of PEAKS Online. View Image -
Figure 13.10.3 The de novo sequencing results can be seen under the Results tab. View Image -
Figure 13.10.4 The page displaying the overall results for one data file submitted. View Image -
Figure 13.10.5 The peptide‐spectrum alignment image helps a user to judge the quality of the result. View Image
Videos
Literature Cited
| 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. | |
| Pevstov, S., Fedulova, I., Mirzaei, H., Buck, C., and Zhang, X. 2006. Performance evaluation of existing de novo sequencing algorithms. J. Proteome Res. 5:3018‐3028. | |
| Steen, H. and Mann, M. 2004. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5:699‐711. | |
| Xu, C. and Ma, B. 2006. Software for computational peptide identification from MS/MS. Drug Discov. Today 11:595‐600. | |
| Zubarev, R.A., Zubarev, A.R., and Savitski, M.M. 2008. Electron capture/transfer versus collisionally activated/induced dissociations: Solo or duet? J. Am. Soc. Mass Spectrom. 19:753‐761. | |
| Internet Resources | |
| http://bioinfor.com/peaksonline | |
| PEAKS Online is freely available. | |
| http://bioinfor.com/peaks | |
| Trial versions of PEAKS Studio and PEAKS Client are available upon request. |
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