Overall workflow for the iPhos-facilitated comprehensive phosphoproteome investigation. This figure is the sketch plot of the overall iPhos-facilitated phosphorylated peptide identification and quantification work-flow. The input and output file formats for different modules are shown in grey. The key integrative tools, collectively called iPhos, to facilitate the workflow are highlighted in (a)-(d). (a) iPhos Peak Extraction Assister automates the msInspect-based batch mode peak extraction. (b) iPhos Module-1 processes the LC-MS data for phosphopeptide signal extraction. (c) iPhos Module-2 generates customized inclusion lists for subsequent targeted LS-MS/MS analysis. (d) iPhos Module-3 links the results of phosphopeptide identification with pattern-based label-free quantitative analysis.