Qualitative and quantitative data obtained on micro and nanovesicle enriched fractions isolated from four citrus species, C. sinensis, C. limon, C. paradisi and C. aurantium are presented. It includes physiochemical characterization by transmission electron microscopy (TEM) and dynamic laser scattering (DLS); and molecular characterization of the biocargo of citrus vesicles by quantitative label-free proteomics. Vesicular transport related proteins of C. sinensis were predicted by (i) finding orthologues based on previously described vesicular transport proteins and (ii) GO term enrichment analysis. Based on the protein content different types of intra and intercellular vesicles were dissected and the distribution of different Enzyme classes (ECs) were determined. This data article is related to “Protein biocargo of citrus fruit-derived vesicles reveals heterogeneous transport and extracellular vesicle populations” (Pocsfalvi et al., 2018).
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