Medicago truncatula proteomics for systems biology: Novel rapid shotgun LC-MS approach for relative quantification based on full-scan selective peptide extraction (Selpex)

M Angeles Castillejo, Christiana Staudinger, Volker Egelhofer, Stefanie Wienkoop

    Publications: Contribution to bookChapterPeer Reviewed

    Abstract

    Medicago truncatula has become the focus of systems biology research for improved legume crop breeding. In plant systems biology, several comparative studies have been carried out using liquid chromatography shotgun mass spectrometry (LC-MS/MS) and database-dependent protein identification analyses in combination with the spectral count for relative quantification. In order to receive optimal protein identification rates and spectral count quantification, data-dependent tandem mass spectrometry with LC separation of more than 1 h is required. Thus LC-MS/MS analyses time is the bottleneck for high-throughput research of experiments with high sample number.We describe a novel method, called full-scan (FS) selective peptide extraction, that allows for comparative quantification of target peptides combined with a significant reduction in LC-MS analysis time. In future, it will be a useful tool to detect (15)N-labeled selected peptide patterns for the targeted analysis of protein turnover and synthesis. We provide a first reference library of selected target peptides generated for M. truncatula leaf tissue. These peptides are also suitable candidates for selective reaction monitoring approaches.
    Original languageEnglish
    Title of host publicationPlant Proteomics
    Subtitle of host publicationMethods and Protocols
    PublisherHumana Press, Inc.
    Pages303-313
    Number of pages11
    Volume1072
    ISBN (Electronic)978-1-62703-631-3
    ISBN (Print)ISBN 978-1-62703-630-6
    DOIs
    Publication statusPublished - 2014

    Publication series

    SeriesMethods in Molecular Biology
    Volume1072
    ISSN1064-3745

    Austrian Fields of Science 2012

    • 106037 Proteomics
    • 106023 Molecular biology

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