Prokaryotic Proteogenomics. Prokaryotic Proteogenomics

Genome annotations are often insufficient, mostly containing predictions based primarily on DNA sequence and not experimental evidence. Proteogenomics is the use of experimental proteomics data to re-evaluate protein sequence predictions. In this project, tandem mass spectrometry data are used to identify peptides sequences from a six-frame translation of the genome. Peptides are subsequently mapped to their genomic coordinates and grouped within an open reading frame. Proteomic evidence is then compared to the public genome annotation, and any novel coding region is reflected in an updated annotation. Data and analysis for the project come from the Biological Separations and Mass Spectrometry group at Pacific Northwest National Laboratory (http://omics.pnl.gov/). Data was obtained in the Environmental Molecular Sciences Laboratory, a U.S. Department of Energy/ Biological and Environmental Research national scientific user facility. Pacific Northwest National Laboratory is operated for the DOE by Battelle under Contract DE-AC05-76RLO 1830. Analysis was performed under a grant from the National Science Foundation, EF- 0949047.