Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.

ABSTRACT: Recent advances in mass spectrometry (MS) have led to increased applications of shotgun proteomics to the refinement of genome annotation. The typical "proteo-genomic" workflows rely on the mapping of peptide MS/MS spectra onto databases derived via six-frame translation of the genome sequence. These databases contain a large proportion of spurious protein sequences which make the statistical confidence of the resulting peptide spectrum matches difficult to assess. Here we performed a comprehensive analysis of the Escherichia coli proteome using LTQ-Orbitrap MS and mapped the corresponding MS/MS spectra onto a six-frame translation of the E. coli genome. We hypothesized that the protein-coding part of the E. coli genome approaches complete annotation and that the majority of six frame-spec

SUBMITTER: Krug K 

PROVIDER: S-EPMC3820952 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature