Figure 2.

Quantitative time-course study of the proteome and phosphoproteome of Arabidopsis seedlings upon cold stress. (A) Numbers of proteins containing one or more p-sites. (B) Venn diagram comparing high-confidence p-sites in this study with class I p-sites identified in a recent Arabidopsis phosphoproteome [30]. (C) Number of total quantified and cold-responsive phosphopeptides. The cold-responsive phosphopeptides were determined using the cutoff of fold change > 2 or <0.5 and adjusted p value < 0.01. (D) Coefficient of variation (CV) values distribution calculated for each phosphopeptide for each four replicates. (E) PCA analysis of the phosphoproteomics data. (F) CV values distribution calculated for each protein for each four replicates. (G) PCA analysis of the global proteomics data. (H) Volcano plots showing upregulated and downregulated phosphopeptides in response to different periods of cold stress. (I) Venn diagram showing phosphopeptides significantly differentially regulated by different periods of cold stress.