Phospho-site specific antibodies become increasingly available, enabling the study of signaling events by Western blotting (WB) or intracellular flow cytometry (Phospho-Flow). Here we compared data generated by WB or Phospho-Flow regarding the kinetics and degree of phosphorylation of membrane proximal TCR signaling molecules. Phosphorylation events in Jurkat T cells were triggered by anti-CD3 stimulation (OKT3) or by oxidative stress (H(2)O(2)) and were analyzed by Phospho-Flow or WB. Both techniques showed that OKT3- or H(2)O(2)-induced, transient phosphorylation of ZAP70 or LAT was dependent on functional Lck. Phospho-Flow data revealed differences in the kinetics and the degree of H(2)O(2)- or OKT3-mediated protein phosphorylation compared with WB data. In addition, using Phospho-Flow we discovered that H(2)O(2)-induced phosphorylation of TCR signaling proteins was inhibited by small molecular weight kinase inhibitors far more potently than OKT3-triggered protein phosphorylation, despite a superior induction of phosphorylation by H(2)O(2). This finding was confirmed by WB. Interestingly, we identified by Phospho-Flow that, in P116 Jurkat cells lacking ZAP70 protein expression, H(2)O(2) potently triggered the phosphorylation of ZAP70 residues Y493 and Y292 but not Y319. The phosphorylation of these ZAP70 tyrosine residues cells was blocked by an Lck inhibitor, suggesting the existence of an Lck-coupled truncated ZAP70 protein or a novel isoform of ZAP70 in P116 cells. Phospho-Flow is a largely quantitative technology with excellent throughput, highly suited in studying the function or inhibition of TCR signaling pathways and allowing the detection of novel pathway insights. It can serve as a good complement to Western blot analysis.