How to aviod Spikes in the buffer flow?

After immobilization, I have tried to equilibrium the system by injecting the running buffer at flow rate of 60ul/min for 40 mins. The sensogram 2-1 (2-protein , 1-blank as reference) shows spikes on every 500s. Isn't strange?, Both Fc-1 and Fc-2 also looks similar. there were spikes in every 500th second. What I can get from this. After this also I could not avoid the spikes in the pump strokes at the time of experiments. I gave 5 mins of stabilization time for every cycle, still the spikes appeared again.

It is not strange. Your pump is 500 ul and flow is 60 ul so every (500/60)*60 seconds the has to be refilled. Then the flow stops for some seconds and because of that (and because ch1 en 2 are in series) the spike appears. You cannot avoid them.

Thank you Arnoud.
If this is the case, by looking at the image attached, can you say the system is equlibriated?

Your system looks properly equilibrated. When you perform your experiment with double referencing (reference subtraction and blank injection subtraction; www.sprpages.nl/experiments/data-processing ) your data will be fine.