We present a simple method to resolve discrete intensity shifts from time-resolved single-molecule emission data. This new method uses multiples of the standard deviation of the measured intensities that are integrated into short time bins. By applying the technique to trimeric units of the main light-harvesting complex (LHCII) of plants, it is shown that the amount of information that can be extracted from an intensity time trace increases considerably, thereby enlarging the possibility to reveal new phenomena. It is demonstrated how shot noise can lead to substantial deviations and misleading interpretations when the conventional two-state kinetic model for intensity fluctuations is applied. By first resolving the accessed intensity levels, the artifactual effect of shot noise is sufficiently reduced. The technique is particularly applicable to the analysis of fluorescence intermittency from multichromophoric systems.