Mass cytometry allows for the use of highly multiplexed antibody panels due to the lack of spill-over between channels detected by mass spectrometry. An advantage over fluorescence cytometry is the relative lack of background, which provides excellent resolution for detection of phosphoproteins and quantification of cell signaling. We have applied mass cytometry to the analysis of whole blood staining after ex vivo stimulation with peanut allergen (Tordesillas et al., J Allergy Clin Immunol 138:1741–4.e9, 2016). This allows for high-dimensional analysis of basophil activation, and analysis of the entire composition of the blood compartment in response to allergen exposure. Here, we describe our optimized protocol for activation and staining of whole blood for mass cytometry analysis that is currently in use in multicenter clinical trials. The protocol can be easily adopted to analyze blood leukocytes in other diseases, including asthma.