Characterizing the chemical composition of microarray features is a difficult yet important task in the production of in situ-synthesized microarrays. Here, we describe it method to determine the chemical composition of microarray features, directly oil the feature. This method utilizes nondiffusional chemical cleavage from the surface along with techniques from MALDI-MS tissue imaging, thereby making the chemical characterization of high-density microarray features simple, accurate, and amenable to high-throughput.