A novel adaptive and approximate shift-invariant wavelet packet feature extraction scheme for event-related potentials (ERPs) in the electroencephalogram (EEG) is introduced in this paper. In this algorithm, the shift-invariant wavelet packed decomposition is done by integrating a cost function for decimation decision in each sub-band expansion. Additionally, a shape adaptation of the wavelet is implemented to find the best adapted wavelet shape for a given class of ERPs. This scheme is used to analyze the time course of the impact of single-pulse transcranial magnetic stimulation (TMS) to the auditory ERPs. We show that the proposed scheme is able to extract even slightest impacts of TMS, making it a promising tool for the extraction of weak ERPs components, particularly in hybrid TMS-EEG/ERP setups.