Diseases including cancers and infections perturb cellular signaling. Mass cytometry provides a readout for up to 52 simultaneous measurements, both of those disease-induced perturbations and importantly of counter-perturbations induced by candidate therapeutics. Furthermore, the simultaneous inclusion of cell phenotype and cell cycle provide a more detailed picture than possible before. After cells are stained with antibodies and other metallic assay reagents, they are introduced into the mass cytometer as a stream of single cells, then atomized and ionized as they pass through the inductively coupled plasma (ICP) torch. Low-mass elements (including carbon and nitrogen) are filtered out by a radio frequency quadrupole before entering the time-of-flight (TOF) detector. A high-speed, online analysis system produces data equivalent to that of traditional fluorescence-based cytometry.