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Gene Model Detection Using Mass Spectrometry

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Book cover Proteome Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 604))

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/.

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Acknowledgments

The project was supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, grant number #2006-35600-17688. It was partially funded by a grant from the National Science Foundation (EPS-0556308-06040293).

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Authors and Affiliations

  1. College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi State, USA

    Bindu Nanduri, Mark L. Lawrence & Shane C. Burgess

  2. Institute for Digital Biology, Mississippi State University, Starkville, Mississippi State, USA

    Bindu Nanduri, Mark L. Lawrence & Shane C. Burgess

  3. Department of Computer Science and Engineering, the Institute for Digital Biology, Mississippi State University, Starkville, Mississippi State, USA

    Nan Wang, Mark L. Lawrence & Susan M. Bridges

  4. Life Sciences and Biotechnology Institute, Mississippi State University, Starkville, Mississippi State, USA

    Mark L. Lawrence & Shane C. Burgess

Authors
  1. Bindu Nanduri
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  2. Nan Wang
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  3. Mark L. Lawrence
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  4. Susan M. Bridges
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  5. Shane C. Burgess
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Corresponding author

Correspondence to Shane C. Burgess .

Editor information

Editors and Affiliations

  1. Fac. Life Sciences, University of Manchester, Oxford Rd., Manchester, M13 9PT, United Kingdom

    Simon J. Hubbard

  2. Fac. Veterinary Science, University of Liverpool, Liverpool, L69 7ZJ, United Kingdom

    Andrew R. Jones

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© 2010 Humana Press, a part of Springer Science+Business Media, LLC

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Nanduri, B., Wang, N., Lawrence, M.L., Bridges, S.M., Burgess, S.C. (2010). Gene Model Detection Using Mass Spectrometry. In: Hubbard, S., Jones, A. (eds) Proteome Bioinformatics. Methods in Molecular Biology™, vol 604. Humana Press. https://doi.org/10.1007/978-1-60761-444-9_10

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  • DOI: https://doi.org/10.1007/978-1-60761-444-9_10

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-443-2

  • Online ISBN: 978-1-60761-444-9

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