Poster Sessions

PROT-2

Gelio Alves

G. Alves, A. Ogurtsov, S. Kowk, W. Wu, G. Wang, R.-F. Shen, Y.-K. Yu

Detection of Co-eluted Peptides using Database Search Methods

Current experimental techniques, especially those applying liquid chromatography mass spectrometry, limit the confidence in protein identification and quantification. Most experimental procedures select only the strongest parent ion in a given mass MS scan for tandem fragmentation (MS2) and all the other co-eluted peptides that have similar chromatographic retention times are ignored and their information lost. We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the strongest two or three parent ions in a given MS scan. A set of spectra with minimal bias towards any of the database search methods used is created to simulate the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods - SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS - in identifying true peptides from superimposed spectra of co-eluted peptides. We show that all the database search methods will gain eventually in the number of true peptide identified by using the compound spectra of co-eluted peptides. In terms of gain in peptide identification, X!Tandem and RAId_DbS seem to benefit more from the compound spectra than other three database search methods. keywords: co-eluted peptides, database search method, peptide identication, proteomics,