I have never pursued this issue you are poining out, but I guess you could use something like a regenerated cellulose centrifugation filter with high molecular cut-off like e.g. Amicon Utra-15 100.000 NMWL by Millipore (#UFC9-100-24).

By performing centrifugation of your media with this filter device you should be able to get rid of the excessive amount of protein in your sample.

The final result depends towards this aim on what cells you are using and what kind of proteins they are producing or secreting.

Antibodies produced by Hybridoma or other extremely massive proteins like mucines will be retained even by a 100 kDa filter, but all smaller proteins like BSA from fetal calf serum for medium conditioning should be eliminated.

I have no idea how viable the cells will be after this procedure, if you need them to be.

Maybe you have to perform at low centrifugation speed for short periods and immediately refill/resuspend the retained cells with solution or unconditioned media.

I have used eppendorf filter tubes before to clean up samples, main down fall is you may have to add more solute to the supernatent to wash it through, in turn diluting the filtrate.

You can get these down to ~10kDa, so can adapt to your experiment

Thanks Cristoph and Jason, your answers are useful. I found 100KDa Amicon, this might be useful but this left proteins might still be a problem in my case. I'll have to deal with them and try to improve protein depletion.

Hi, you can use even 10kDa on the supernatant, I use generally these ones for deproteinization, but keep in mind that still you will have some protein presence between 10-30 kDa, if you need a total de-prot you can use an acid precipitation (if you do not have to use again on your cells of course)

I known it is not very specific but you could add sepharose or agarose beads to the supernatant in order to remove the left over proteins from your first depletion step.