A method for a mass spectrometric determination of contaminant components of a thin oxide surface layer of a semiconductor wafer use a movable mechanical stage to scan and raster a large area of the wafer in a continuous scanning motion. The mass of analyte is greatly increased, resulting in improved sensitivity to trace components in the surface layer by a factor of 10-100 or more. A light beam interferometer is used to determine non-planarity from e.g., warping of the wafer and provide a correction by maintaining a constant separation between the wafer and the extraction plate or adjusting the electrical bias of the wafer relative to the extraction bias.