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PMID: 17122065 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Review

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

Journal of biomolecular techniques : JBT ·Vol. 17 ·No. 5 ·2006-12-00 ·Pages 327-32

Rohrbough JG, Breci L, Merchant N, Miller S, Haynes PA

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.

MeSH Terms
Algorithms Databases, Protein Oryza/chemistry Peptides/analysis,chemistry Plant Proteins/analysis,chemistry Proteins/analysis,chemistry
Chemicals
Peptides Plant Proteins Proteins
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Rohrbough James G
Department of Biochemistry and Molecular Biophysics, The University of Arizona, Tucson, USA.
Breci Linda
Merchant Nirav
Miller Susan
Haynes Paul A
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Article Info
Journal
Journal of biomolecular techniques : JBT
Abbr.
J Biomol Tech
ISSN
1524-0215
Published
2006-12-00
Pages
327-32
Language
English
Region
United States
NLM ID
100888641
PMCID
PMC2291803
Subset
IM
External Links
PubMed source PMC Full Text
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