Single-cell systems biology of cancer requires methods to measure multiple markers within tumors, quantitatively and at single-cell resolution. To this end, the Bodenmiller group has pioneered a single-cell mass spectrometric approach called mass cytometry (CyTOFTM). This technology allows the simultaneous and high-throughput quantification of approximately 50 markers, including proteins and their modifications, on single cells. We employ mass cytometry-based methods to study the cellular composition and regulation of tissue ecosystems, for insights into health and disease.