Identification of proteins from organisms with unsequenced genomes by tandem mass spectrometry and sequence-similarity database searching tools

Adam J. Liska, Andrej Shevchenko

Research output: Chapter in Book/Report/Conference proceedingChapter

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.

Original languageEnglish (US)
Title of host publicationCell Biology
Subtitle of host publicationA Laboratory Handbook
PublisherElsevier
Pages399-407
Number of pages9
ISBN (Print)9780121647308
DOIs
StatePublished - Nov 16 2005
Externally publishedYes

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology

Fingerprint

Dive into the research topics of 'Identification of proteins from organisms with unsequenced genomes by tandem mass spectrometry and sequence-similarity database searching tools'. Together they form a unique fingerprint.

Cite this