Probably it is stuck to the membrane. Try with other filters such as Durapore (PVDF). Your 0.2um pore filter is most likely made from cellulose. You also may try to spin your sample (top bench eppendorf centrifuge), use the supernatant and then load it on the FPLC column. Do check for further information: C. Dicko, D. Knight, J.M. Kenney, F. Vollrath, Biomacromolecules 5 (2004) 758.
Hi Mr Frank, thank you for the opinion and yes you were right that the membrane is made of cellulose. I will resort to.your suggestion based on the paper. Many thanks again.