Differential expression and phosphorylation maps of a LC-MS/MS experiment. (A) The differential expression map of Scenario 2 shows a subset of proteins identified by the LC-MS/MS experiment. The size indicates if the proteins are uniquely (medium size) or commonly differentially expressed (large size) in two pairs of biological states (i.e., in two iTRAQ ratios). The color indicates the type of differential expression: red (green) for up (down) regulation in at least one ratio, yellow for up/down regulation in the two ratios, and blue for no differential expression in any ratio. (A1) Zoomed area of the differential expression comparison map, showing the Biological Process associated with each protein in the spheres labels. (B) The phosphorylation map of Scenario 3 shows all proteins identified by the LC-MS/MS experiment. Large spheres indicate proteins that have undergone phosphorylation, whereas their color (red/green/blue) indicates their up/down/no regulation based on an iTRAQ ratio. (B1) Pop up menu of a right clicked protein, showing its Accession Number, the Spectrum id and the sequence of the corresponding phosphorylated peptide.