Using BiblioSpec for Creating and Searching Tandem MS Peptide Libraries

Barbara Frewen1, Michael J. MacCoss1

1 University of Washington, Seattle, Washington
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.7
DOI:  10.1002/0471250953.bi1307s20
Online Posting Date:  December, 2007
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Abstract

BiblioSpec is a software package for creating and searching libraries of tandem MS peptide spectra. Library searching provides a quick method for making peptide‐spectrum matches by comparing a query spectrum to a collection of reference spectra of known peptide sequence. Pre‐assembled libraries for several model organisms can be used as the basis of a search or custom libraries can easily be assembled. The protocols in this unit describe installing BiblioSpec, searching libraries, and creating custom libraries. Curr. Protoc. Bioinform. 20:13.7.1‐13.7.12. © 2007 by John Wiley & Sons, Inc.

Keywords: proteomics; peptide spectrum library; peptide identification

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Using BlibSearch to Make Peptide Identifications
  • Support Protocol 1: Downloading and Installing BiblioSpec
  • Support Protocol 2: Using BlibBuild to Construct a Mass Spectrum Library
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

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Literature Cited

Literature Cited
   Craig, R., Cortens, J.C., Fenyo, D., and Beavis, R.C. 2006. Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 5:1843‐1849.
   Frewen, B.E., Merrihew, G.E., Wu, C.C., Noble, W.S., and MacCoss, M.J. 2006. Analysis of peptide MS/MS spectra from large‐scale proteomics experiments using spectrum libraries. Anal. Chem. 78:5678‐5684.
   Heller, S. 1972. Conversational mass spectral retrieval system and its use as an aid in structure determination. Anal. Chem. 44:1951‐1961.
   Lam, H., Deutsch, E.W., Eddes. J.S., Eng, J.K., King, N., Stein, S.E., and Aebersold, R. 2007. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7:655‐667.
   Liu, J., Bell, A.W., Bergeron, J.J., Yanofsky, C.M., Carrillo, B., Beaudrie, C.E., and Kearney, R.E. 2007. Methods for peptide identification by spectral comparison. Proteome Sci. 5:3.
   McDonald, W.H., Tabb, D.L., Sadygov, R.G., MacCoss, M.J., Venable, J., Graumann, J., Johnson, J.R., Cociorva, D., and Yates, J.R., 3rd. 2004. MSI, MS2, and SQT‐three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom. 18:2162‐2168.
   Stein, S.E. and Scott, D.R. 1994. Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 5:859‐866.
   Yates, J.R. 3rd, Morgan, S.F., Gatlin, C.L., Griffin, P.R., and Eng, J.K. 1998. Method to compare collision‐induced dissociation spectra of peptides: Potential for library searching and subtractive analysis. Anal. Chem. 70:3557‐3565.
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