A study is presented of the factors affecting the calibration of the mass scale for time-of-flight SIMS (TOF-SIMS). The effect of the ion kinetic energy, emission angle and other instrumental operating parameters on the measured peak position are determined. This shows clearly why molecular and atomic ions have different relative peak positions and the need for an aperture to restrict ions at large emission angles. A calibration protocol is developed which gives a fractional mass accuracy of better than 10 ppm for masses up to 140 u. The effects of extrapolation beyond the calibration range are discussed and a recommended procedure is given to ensure that accurate mass is achieved within a selectable uncertainty for large molecules. Crown Copyright (c) 2006 Published by Elsevier B.V. All rights reserved.