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De Novo Interpretation of Tandem Mass Spectra

Bin Ma¹, Gilles Lajoie²

¹University of Waterloo, Waterloo, Ontario, Canada
²University of Western Ontario, London, Ontario, Canada

Publication Name:

Current Protocols in Bioinformatics

Unit Number:

Unit 13.10

DOI:

10.1002/0471250953.bi1310s25

Online Posting Date:

March, 2009

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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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Introduction
Basic Principles
Basic Protocol: Auto De Novo Sequencing with PEAKS Software
Alternate Protocol: De Novo Sequencing with PEAKS Studio or Client
Guidelines for Understanding Results
Commentary
Literature Cited
Figures

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Figures

Figure 13.10.1

The spectrum contains clear y-ion ladders, which can be used to derive the peptide sequence.

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Figure 13.10.2

The input page of PEAKS Online.

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Figure 13.10.3

The de novo sequencing results can be seen under the Results tab.

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Figure 13.10.4

The page displaying the overall results for one data file submitted.

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Figure 13.10.5

The peptide-spectrum alignment image helps a user to judge the quality of the result.

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Literature Cited

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.