UNIT 25.5 Using Spectral Libraries for Peptide Identification from Tandem Mass Spectrometry (MS/MS) Data

Abstract

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.