De Novo Interpretation of Tandem Mass Spectra

Bin Ma1, Gilles Lajoie2

1 University of Waterloo, Waterloo, Ontario, Canada, 2 University 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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Table 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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Materials

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Figures

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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