UNIT 25.2 Overview of Tandem Mass Spectrometry (MS/MS) Database Search Algorithms

Abstract

Mass spectrometry–based methods for the identification of proteins are fundamental platform technologies for proteomics. One comprehensive approach is to subject trypsinized peptides to tandem mass spectrometry (MS/MS) to obtain detailed structural information. Different strategies are available for interpreting MS/MS data and hence deducing the amino acid sequence of the peptides. The most common method is to use a search algorithm to identify peptides by correlating experimental and theoretical MS/MS data (the latter being generated from possible peptides in the protein sequence database). Identified peptides are collated and protein entries from the sequence database inferred. This unit focuses on the most widely used tandem MS peptide identification search algorithms (commercial and open source), their availability, ease of use, strengths, speed and scoring, as well as their relative sensitivity and specificity. Curr. Protoc. Protein Sci. 49:25.2.1-25.2.19. © 2007 by John Wiley & Sons, Inc.