Verification of single-peptide protein identifications by the application of complementary database search algorithms

James G. Rohrbough, Linda Breci, Nirav C Merchant, Susan Miller, Paul A. Haynes

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Data produced from the MudPIT analysis of yeast (S. cerevisiae) and rice (O. sativa) were used to develop a technique to validate single-peptide protein identifications using complementary database search algorithms. This results in a considerable reduction of overall false-positive rates for protein identifications; the overall false discovery rates in yeast are reduced from near 25% to less than 1%, and the false discovery rate of yeast single-peptide protein identifications becomes negligible. This technique can be employed by laboratories utilizing a SEQUEST-based proteomic analysis platform, incorporating the XTandem algorithm as a complementary tool for verification of single-peptide protein identifications. We have achieved this using open-source software, including several data-manipulation software tools developed in our laboratory, which are freely available to download.

Original languageEnglish (US)
Pages (from-to)327-332
Number of pages6
JournalJournal of Biomolecular Techniques
Volume17
Issue number5
StatePublished - Dec 2006

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Databases
Peptides
Yeasts
Proteins
Software
Proteomics
Saccharomyces cerevisiae
Oryza

Keywords

  • Database search algorithms
  • Protein identification
  • SEQUEST criteria
  • Single-peptide verification
  • Tandem mass spectrometry
  • Xtandem

ASJC Scopus subject areas

  • Molecular Biology
  • Medicine(all)

Cite this

Verification of single-peptide protein identifications by the application of complementary database search algorithms. / Rohrbough, James G.; Breci, Linda; Merchant, Nirav C; Miller, Susan; Haynes, Paul A.

In: Journal of Biomolecular Techniques, Vol. 17, No. 5, 12.2006, p. 327-332.

Research output: Contribution to journalArticle

Rohrbough, James G. ; Breci, Linda ; Merchant, Nirav C ; Miller, Susan ; Haynes, Paul A. / Verification of single-peptide protein identifications by the application of complementary database search algorithms. In: Journal of Biomolecular Techniques. 2006 ; Vol. 17, No. 5. pp. 327-332.
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