Objective: A fundamental issue in EEG event-related potentials (ERPs) studies is the amount of data required to have an accurate ERP model. This also impacts the time required to train a classifier for a brain-computer interface (BCI). This issue is mainly due to the poor signal-to-noise ratio, and to the large fluctuations of the EEG caused by several sources of variability. One of these sources is directly related to the experimental protocol or application designed, and may affect to amplitude or latency variations. This usually prevents BCI classifiers to generalize among different experimental protocols. In this work, we analyze the effect of the amplitude and the latency variations among different experimental protocols based on the same type of ERP. Approach: We present a method to analyze and compensate for the latency variations in BCI applications. The algorithm has been tested on two widely used ERPs (P300 and observation error potentials), in three experimental protocols in each case. We report the ERP analysis and single-trial classification. Results and significance: The results obtained show (i) how the experimental protocols significantly affect the latency of the recorded potentials but not the amplitudes, and (ii) how the use of latency-corrected data can be used to generalize the BCIs, reducing this way the calibration time when facing a new experimental protocol.