Time-of-flight secondary ion mass spectrometry (ToF-SIMS) data collected in single ion counting mode suffers from dead-time effects that lead to potentially confusing artefacts when common multivariate analysis (MVA) methods are applied to the data. These artefacts can be eliminated by applying an advanced Poisson dead-time correction that accounts for the signal intensity in the dead-time window preceding each time channel. Because this correction is nonlinear, it changes the noise distribution in the data. In this work, the accuracy of this dead-time correction and the noise characteristics of the corrected data have been analysed for spectra with small numbers of primary ion pulses. A simple but accurate equation for estimating the standard deviation in the advanced dead-time corrected data has been developed. Based on these results, a scaling procedure to enable successful MVA of advanced dead-time corrected ToF-SIMS data has been developed. The improvements made possible by using the advanced dead-time correction and our recommended scaling are presented for principal components analysis of a ToF-SIMS image of aerosol particles on polytetrafluoroethylene. Recommendations are made for using the advanced dead time correction and scaling ToF-SIMS data in order optimize the outcomes of MVA. Copyright © 2014 John Wiley & Sons, Ltd.