Reducing chemical contaminants is increasingly important for maintaining competitive production costs during fabrication of electronic devices. There is currently no production floor capability for mapping chemical contaminants across an electronic device substrate on a routine basis. A scanning surface chemical analyzer for mapping the distributions of a variety of chemicals on substrates is disclosed. The analyzer includes an array of sensors, each of which detects a single chemical or narrow range of chemicals, a scanning mechanism to provide a mapping capability, an electrical signal analyzer to collect and analyze signals from the array of sensors and generate reports of chemical distributions, and an optical desorption mechanism to amplify detection. A preferred embodiment includes an array of miniature quadrupole mass spectrometers in the sensor array. Scanning modes include whole substrate mapping, region sampling, and spot sampling of known defect sites.