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Deviation from the mobile proton model in amino-modified peptides: implications for multiple reaction monitoring analysis of peptides

Authors

  • Steven J. Locke,

    1. Institute for Marine Biosciences, National Research Council of Canada, 1411 Oxford St., Halifax, Nova Scotia, Canada B3H 3Z1
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  • Andrew D. Leslie,

    1. Institute for Marine Biosciences, National Research Council of Canada, 1411 Oxford St., Halifax, Nova Scotia, Canada B3H 3Z1
    2. Dalhousie University, Department of Chemistry, Halifax, Nova Scotia, Canada B3H 4J3
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  • Jeremy E. Melanson,

    1. Institute for Marine Biosciences, National Research Council of Canada, 1411 Oxford St., Halifax, Nova Scotia, Canada B3H 3Z1
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  • Devanand M. Pinto

    Corresponding author
    1. Institute for Marine Biosciences, National Research Council of Canada, 1411 Oxford St., Halifax, Nova Scotia, Canada B3H 3Z1
    2. Dalhousie University, Department of Chemistry, Halifax, Nova Scotia, Canada B3H 4J3
    • Institute for Marine Biosciences, National Research Council of Canada, 1411 Oxford St., Halifax, Nova Scotia, Canada B3H 3Z1.
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  • Dedicated to Dr. Robert Boyd on the occasion of his retirement as Editor-in-Chief of Rapid Communications in Mass Spectrometry.

Abstract

The study of peptide fragmentation is important to the understanding of chemical processes occurring in the gas phase and the more practical concern of peptide identification for proteomic analysis. Using the mobile proton model as a framework, we explore the effect of amino-group modifications on peptide fragmentation. Three aldehydes are used to transform the peptides' primary amino groups into either a dimethylamino or a heterocyclic structure (five- or six-membered). The observed fragmentation patterns deviate strongly from those observed for the analogous underivatised peptides. In particular, the a1 ion is the base peak in most tandem mass spectra of the derivatised peptides. The a1 ion intensity depends strongly on the N-terminal amino acid, with tyrosine and phenylalanine having the strongest enhancement. Despite the change in fragmentation patterns of the derivatised peptides, they still provide high-quality tandem mass spectra that, in many cases, are more amenable to database searching than the spectra of underivatised peptides. In addition, the reliable presence of the a1 ion facilitates rapid quantitative measurements using the multiple reaction monitoring approach. Copyright © 2006 John Wiley & Sons, Ltd.

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