Using Spectral Libraries for Peptide Identification from Tandem Mass Spectrometry (MS/MS) Data

Henry Lam1, Ruedi Aebersold2

1 Hong Kong University of Science and Technology, Kowloon, Hong Kong, 2 Institute for Systems Biology, Seattle, Washington
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 25.5
DOI:  10.1002/0471140864.ps2505s60
Online Posting Date:  April, 2010
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Spectral library searching is an emerging approach in proteomic data analysis for the inference of peptide identifications from tandem mass spectra. It offers a promising alternative to sequence database searching, currently the dominant method for this purpose. In spectral searching, a spectral library is first meticulously compiled from a large collection of previously observed and identified peptide MS/MS spectra. The spectrum of the unknown peptide can then by identified by comparing it to all the candidates in the spectral library for the best match. This unit covers the basic principles of spectral searching, describes its advantages and limitations, and reviews the available software tools developed for spectral library searching and building, in terms of their algorithms and their surrounding informatics support. Curr. Protoc. Protein Sci. 60:25.5.1‐25.5.9. © 2010 by John Wiley & Sons, Inc.

Keywords: spectral library; spectral searching; X!Hunter; Bibliospec; SpectraST; NIST MS search

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Table of Contents

  • Background
  • Advantages and Limitations of Spectral Searching
  • Spectral Search Engines
  • Libraries
  • Conclusions
  • Acknowledgment
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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