Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
James Lyons-Weiler
Bioinformatics Analysis Core, Genomics and Proteomics Core Laboratories,
Pittsburgh, PA
Tanzania
Research Article
Evaluation of the Consensus of Four Peptide Identification Algorithms for Tandem Mass Spectrometry Based Proteomics
Author(s): Ruben K. Dagda, Tamanna Sultana and James Lyons-WeilerRuben K. Dagda, Tamanna Sultana and James Lyons-Weiler
The availability of different scoring schemes and f ilter set- tings of protein database search algorithms has gre atly ex- panded the number of search methods for identifying candi- date peptides from MS/MS spectra. We have previousl y shown that consensus-based methods that combine thr ee search algorithms yield higher sensitivity and spec ificity com- pared to the use of a single search engine (individ ual method). We hypothesized that union of four search engines ( Sequest, Mascot, X!Tandem and Phenyx) can further enhance sen- sitivity and specificity. ROC plots were generated to mea- sure the sensitivity and specificity of 5460 consen sus meth- ods derived from the same dataset. We found that Ma scot outperformed individual methods for sensitivity and speci- ficity, while Phenyx performed the worst. The union con- sensus methods generally produced.. View More»
DOI:
10.4172/jpb.1000119