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Phosphoproteomic Data Analysis. A, Venn diagram describing the phosphopeptides identified by mass spectrometry in PC12(c) and PTR(s) with a peptide false positive rate of 0.5%. B, Distribution of the log (ratio) of the sample PC12(c) normalized against the log (ratio) of the peptides from the PTR(s) sample. Each phosphopeptide with a log (ratio) above 0.25 or below –0.25 represents a down-regulated or up-regulated modification because of stimulation, respectively.
