Calibrating E-values for MS2 database search methods.

ABSTRACT:

Background

The key to mass-spectrometry-based proteomics is peptide identification, which relies on software analysis of tandem mass spectra. Although each search engine has its strength, combining the strengths of various search engines is not yet realizable largely due to the lack of a unified statistical framework that is applicable to any method.

Results

We have developed a universal scheme for statistical calibration of peptide identifications. The protocol can be used for both de novo approaches as well as database search methods. We demonstrate the protocol using only the database search methods. Among seven methods -SEQUEST (v27 rev12), ProbID (v1.0), InsPecT (v20060505), Mascot (v2.1), X!Tandem (v1.0), OMSSA (v2.0) and RAId_DbS - calibrated, except for X!Tandem and

SUBMITTER: Alves G 

PROVIDER: S-EPMC2206012 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature