Gene model detection using mass spectrometry.

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

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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 www.agbase.msstate.edu/tools/ .

Original languageEnglish (US)
Pages (from-to)137-144
Number of pages8
JournalMethods in molecular biology (Clifton, N.J.)
Volume604
StatePublished - 2010
Externally publishedYes

Fingerprint

Mass Spectrometry
Genome
Open Reading Frames
Proteomics
Genes
Workflow
Sequence Analysis
Proteins
Peptides
Research
Proteogenomics

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Nanduri, B., Wang, N., Lawrence, M. L., Bridges, S. M., & Burgess, S. C. (2010). Gene model detection using mass spectrometry. Methods in molecular biology (Clifton, N.J.), 604, 137-144.

Gene model detection using mass spectrometry. / Nanduri, Bindu; Wang, Nan; Lawrence, Mark L.; Bridges, Susan M.; Burgess, Shane C.

In: Methods in molecular biology (Clifton, N.J.), Vol. 604, 2010, p. 137-144.

Research output: Contribution to journalArticle

Nanduri, B, Wang, N, Lawrence, ML, Bridges, SM & Burgess, SC 2010, 'Gene model detection using mass spectrometry.', Methods in molecular biology (Clifton, N.J.), vol. 604, pp. 137-144.
Nanduri, Bindu ; Wang, Nan ; Lawrence, Mark L. ; Bridges, Susan M. ; Burgess, Shane C. / Gene model detection using mass spectrometry. In: Methods in molecular biology (Clifton, N.J.). 2010 ; Vol. 604. pp. 137-144.
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