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J Biomol Tech. 2006 Dec;17(5):327-32.

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

Author information

1
Department of Biochemistry and Molecular Biophysics, The University of Arizona, Tucson, USA.

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.

PMID:
17122065
PMCID:
PMC2291803
[Indexed for MEDLINE]
Free PMC Article

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