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Proteogenomics

Authors

  • Santosh Renuse,

    1. Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
    2. Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala, India
    3. McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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  • Raghothama Chaerkady,

    1. Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
    2. McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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  • Akhilesh Pandey

    Corresponding author
    1. McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    2. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    3. Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    • McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA Fax: +1-410-502-7544
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  • Colour Online: See the article online to view Figs. 3, 4 and 5 in colour

Abstract

The ability to sequence DNA rapidly, inexpensively and in a high-throughput fashion provides a unique opportunity to sequence whole genomes of a large number of species. The cataloging of protein-coding genes from these species, however, remains a non-trivial task with the majority of initial genome annotation dependent on the use of gene prediction algorithms. Recent advances in mass spectrometry-based proteomics now enable generation of accurate and comprehensive protein sequence of tissues and organisms. Proteogenomics allows us to harness the wealth of information available at the proteome level and apply it to the available genomic information of organisms. This includes identifying novel genes and splice isoforms, assigning correct start sites and validating predicted exons and genes. It is also possible to use proteogenomics to identify protein variants that could cause diseases, to identify protein biomarkers and to study genome variation. We anticipate proteogenomics to become a powerful approach that will be routinely employed by ‘Genome and Proteome Centers’ of the future.

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