How specific is my SRM?: The issue of precursor and product ion redundancy

Authors

  • Jamie Sherman,

    1. Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
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  • Matthew J. McKay,

    1. Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
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  • Keith Ashman,

    1. Centro Nacional de Investigaciones Oncologicas, Proteomic Unit, C/Melchor, Fernandez Almagro, Madrid, Spain
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  • Mark P. Molloy Dr.

    Corresponding author
    1. Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
    • Australian Proteome Analysis Facility, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia Fax: +61-2-9850-6200
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Abstract

Selected reaction monitoring (SRM) MS is proving to be a popular approach for targeted quantitative proteomics. The use of proteotypic peptides as candidates for SRM analysis is a wise first step in SRM method design. The obvious reason for this is the need to avoid redundancy at the sequence level, however this is incidental. The true reason is that homologous peptides result in redundancy in the mass-to-charge domain. This may seem like a trivial subtlety, however, we believe this is an issue of far greater significance than the proteomic community is aware. This VIEWPOINT article serves to highlight the complexity associated with designing SRM assays in light of potential ion redundancy.

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