Illustration of phosphopeptide signal data mining. Three-dimensional (retention time, m/z and signal intensity) representation of the LC-MS signals before and after the signal data mining of iPhos Module-1. (a) Approximately 19,000 monoisotopic signals are in the tryptic pTyr-enriched protein mixture samples that were not alkaline phosphatase treated. (b) The signals in the tryptic pTyr-enriched protein mixture that has undergone alkaline phosphatase dephosphorylation. (c) iPhos Module-1 extracted 262 possible pTyr signals with mass shifts of some multiples of phosphate group loss.