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Halobacterium salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage
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    Halobacterium salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage
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    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, Departments of Biology, Microbiology, and Medicinal Chemistry, University of Washington, Seattle, Washington 98195, and Spielberg Family Center for Applied Proteomics, Cedars-Sinai Medical Center, 8750 West Beverly Boulevard, Los Angeles, California 90048
    * To whom correspondence should be addressed. Nitin S. Baliga, Telephone, 206-732-1266; Fax, 206-732-1299; E-mail, [email protected]
    †Institute for Systems Biology.
    ‡Department of Biology, University of Washington.
    §Current affiliation: Department of Biomedical Engineering and Genome Center, University of California, Davis, One Shields Drive, Davis, California 95616.
    ∥Department of Medicinal Chemistry, University of Washington.
    ⊥Cedars-Sinai Medical Center.
    #Department of Microbiology, University of Washington.
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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2008, 7, 9, 3755–3764
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    https://doi.org/10.1021/pr800031f
    Published July 25, 2008
    Copyright © 2008 American Chemical Society

    Abstract

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    The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

    Copyright © 2008 American Chemical Society

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    Comparative analysis revealed possible similarities between spectral counts and genome organization, a finding discussed in the Supporting Information. Supporting figures (Figure SF-1, Figure SF-2) and Supplementary Tables (ST1 and ST2).This material is available free of charge via the Internet at http://pubs.acs.org.

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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2008, 7, 9, 3755–3764
    Click to copy citationCitation copied!
    https://doi.org/10.1021/pr800031f
    Published July 25, 2008
    Copyright © 2008 American Chemical Society

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