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

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


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms*
  • Databases, Protein*
  • Oryza / chemistry
  • Peptides / analysis*
  • Peptides / chemistry
  • Plant Proteins / analysis
  • Plant Proteins / chemistry
  • Proteins / analysis*
  • Proteins / chemistry


  • Peptides
  • Plant Proteins
  • Proteins