PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data

Figure 2

Volcano plots of results of the STAT1 AP-MS experiment. (a) The mean log₂ ratios of STAT1-Bio with EPO treatment versus GFP-Bio are plotted versus the corresponding values. X proteins are being depicted in red passing the thresholds of value below 0.005 and log₂-FC > 1 and were treated as putative STAT1 binding partners. (b) Analogously the volcano represents the AP-MS analysis of phosphorylated STAT1 versus GFP control. (c) Representation of the STAT1 activation experiments. Proteins which are identified as putative binding partners or which are derived as PPIs from literature are plotted depending on their binding properties to phosphorylated (enriched shown in blue) or nonphosphorylated (enriched shown in red) STAT1 proteins.

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