An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays.

ABSTRACT: New technologies in genomics and proteomics have influenced the emergence of proteogenomics, a field at the confluence of genomics, transcriptomics, and proteomics. First generation proteogenomic toolkits employ peptide mass spectrometry to identify novel protein coding regions. We extend first generation proteogenomic tools to achieve greater accuracy and enable the analysis of large, complex genomes. We apply our pipeline to Zea mays, which has a genome comparable in size to human. Our pipeline begins with the comparison of mass spectra to a putative translation of the genome. We select novel peptides, those that match a region of the genome that was not previously known to be protein coding, for grouping into refinement events. We present a novel, probabilistic framework for evaluating

SUBMITTER: Castellana NE 

PROVIDER: S-EPMC3879611 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature