MultiTag: Multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry

Shamil Sunyaev, Adam J. Liska, Alexander Golod, Anna Shevchenko, Andrej Shevchenko

Research output: Contribution to journalArticlepeer-review

107 Scopus citations

Abstract

The characterization of proteomes by mass spectrometry is largely limited to organisms with sequenced genomes. To identify proteins from organisms with unsequenced genomes, database sequences from related species must be employed for sequence-similarity protein identifications. Peptide sequence tags (Mann, 1994) have been used successfully for the identification of proteins in sequence databases using partially interpreted tandem mass spectra of tryptic peptides. We have extended the ability of sequence tag searching to the identification of proteins whose sequences are yet unknown but are homologous to known database entries. The MultiTag method presented here assigns statistical significance to matches of multiple error-tolerant sequence tags to a database entry and ranks alignments by their significance. The MultiTag approach has the distinct advantage over other sequence-similarity approaches of being able to perform sequence-similarity identifications using only very short (2-4) amino acid residue stretches of peptide sequences, rather than complete peptide sequences deduced by de novo interpretation of tandem mass spectra. This feature facilitates the identification of low abundance proteins, since noisy and low-intensity tandem mass spectra can be utilized.

Original languageEnglish (US)
Pages (from-to)1307-1315
Number of pages9
JournalAnalytical Chemistry
Volume75
Issue number6
DOIs
StatePublished - Mar 15 2003
Externally publishedYes

ASJC Scopus subject areas

  • Analytical Chemistry

Fingerprint

Dive into the research topics of 'MultiTag: Multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry'. Together they form a unique fingerprint.

Cite this