Chapter 51 - Identification of Proteins from Organisms with Unsequenced Genomes by Tandem Mass Spectrometry and Sequence-Similarity Database Searching Tools

Abstract

This chapter focuses on MS BLAST and MultiTag as bioinformatic methods for the identification of proteins by the interpretation of tandem mass spectra of peptides and sequence-similarity searching. Alternatively, in analyses where MultiTag is applied, tandem mass spectra of peptides can be acquired with any ionization source and tandem mass spectrometer that enables the creation of peptide sequence tags. Sequence tags that contain a few confidently designated amino acid residues and mass values that lock the short sequence stretch into the length of the peptide can often be generated from tandem mass spectra with the software packages associated with mass spectrometers. Microsoft Excel or an alternative spreadsheet program is required for compiling of search results before submission to MultiTag. MS BLAST is a specialized BLAST-based tool for the identification of proteins by sequence similarity searching that utilizes peptide sequences produced by the interpretation of tandem mass spectra. Peptide sequences are generated from the interpretation of tandem mass spectra from the analysis of a single in-gel or in-solution digest of an unknown protein, edited and assembled into a query list for the MS BLAST search.