The identification of phosphorylation on proteins has become practicable for many laboratories in recent years, largely due to improvements in mass spectrometry (MS) and the development of methods to selectively enrich for phosphorylated peptides and proteins. However, phosphorylation is a dynamic and reversible modification which plays a central role in many biological processes including intracellular signalling. Therefore, the quantitative analysis of phosphorylated proteins and peptides is a subject of intense interest. We discuss three applications of isobaric tags for relative and absolute quantitation (iTRAQ) to the analysis of phosphopeptides from a variety of sample materials.