MAPA Distinguishes Genotype-Specific Variability of Highly Similar Regulatory Protein Isoforms in Potato Tuber

Wolfgang Höhenwarter (Corresponding author), Abdelhalim Larhlimi, Jan Hummel, Volker Egelhofer, Joachim Selbig, Joost T. van Dongen, Stefanie Wienkoop, Wolfram Weckwerth

    Publications: Contribution to journalArticlePeer Reviewed

    Abstract

    Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers of shotgun proteomics analyses on a personal computer in a matter of hours. We compared 183 LC-MS analyses and more than 2 million MS/MS spectra and could define and separate the proteomic phenotypes of field grown tubers of 12 tetraploid cultivars of the crop plant Solanum tuberosum. Protein isoforms of patatin as well as other major gene families such as lipoxygenase and cysteine protease inhibitor that regulate tuber development were found to be the primary source of variability between the cultivars. This suggests that differentially expressed protein isoforms modulate genotype specific tuber development and the plant phenotype. We properly assigned the measured abundance of tryptic peptides to different protein isoforms that share extensive stretches of primary structure and thus inferred their abundance. Peptides unique to different protein isoforms were used to classify the remaining peptides assigned to the entire subset of isoforms based on a common abundance profile using multivariate statistical procedures. We identified nearly 4000,proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date.
    Original languageEnglish
    Pages (from-to)2979-2991
    Number of pages13
    JournalJournal of Proteome Research
    Volume10
    Issue number7
    Publication statusPublished - 2011

    Austrian Fields of Science 2012

    • 106037 Proteomics
    • 106023 Molecular biology

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