Figure 3

Characterization of phosphopeptides, phosphosites, and phosphoproteins. The 6-10B cells with 48-h DNP treatment were used to identify DNP-regulated serine/threonine phosphorylation of proteins. To assign the phosphorylation sites precisely within a peptide, the PTM score was used to calculate the probabilities of phosphorylation at each site as described in the methods. A, Distribution of peptides with single, double, triple, and quadruple (including higher) phosphorylation peptides. B, Distribution of the Ser, Thr, and Tyr phosphosites in the DNP-regulated phosphoproteome. Phosphopeptides were categorized into class I and class II phosphosites by calculating the probabilities for phosphorylation at each site based on PTM scores. Here, only class I phosphosites (high probability) were used to analyze the distribution. C, Subcellular location of the phosphoproteome in vivo and GO analysis of DNP-regulated phosphoproteome. D, Total phosphoprotein scores of 6-10B cells with or without DNP treatment.