Hi Ahmed,
The spike come from the fact that the channels are in series. When subtracting a reference, both channels are a little out of phase.
In the Biacore you can use the direct referencing during the experiment which will give less spikes.
Or you can adjust the injection time point t=0 for each curve.
When using a program like Scrubber, you kan artificially remove the spikes.
Large spikes occur mainly when the bulk effect is large (>25 RU) and the compensation by the reference channel is not optimal.
Kind regards
Arnoud