Gene model detection using mass spectrometry.

Bindu Nanduri, Nan Wang, Mark L. Lawrence, Susan M. Bridges, Shane C. Burgess

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


The utility of a genome sequence in biological research depends entirely on the comprehensive description of all of its functional elements. Analysis of genome sequences is still predominantly gene-centric (i.e., identifying gene models/open reading frames). In this article, we describe a proteomics-based method for identifying open reading frames that are missed by computational algorithms. Mass spectrometry-based identification of peptides and proteins from biological samples provide evidence for the expression of the genome sequence at the protein level. This proteogenomic annotation method combines computationally predicted ORFs and the genome sequence with proteomics to identify novel gene models. We also describe our proteogenomic mapping pipeline - a set of computational tools that automate the proteogenomic annotation work flow. This pipeline is available for download at .

Original languageEnglish (US)
Pages (from-to)137-144
Number of pages8
JournalMethods in molecular biology (Clifton, N.J.)
StatePublished - 2010

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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