1. A method of analyzing a population of cells, comprising: i) obtaining an array of cells on a substrate, wherein the cells are labeled with one or more mass tags and are separated from one another; ii) measuring, using a plurality of secondary ion mass spectrometry (SIMS) pulses, the abundance of the one or more mass tags at each of a plurality of locations occupied by the cells and at each of a plurality of depths within the cells, thereby generating, for each individual cell measured, a set of data; and iii) outputting the set of data for each of the cells analyzed.