I'll be more specific:
I've been working with a GE HiTrap SP HP ion exchange column (1 ml column volume). My sample is a protein in aqueous solution, to which I add fat-soluble vitamin D, in 100% EtOH; the final sample is 2% EtOH. Some of the vitamin D binds to the protein, and some doesn't. Because vitamin D is highly hydrophobic, the free population tends to aggregate into particles which are often larger than the hydrodynamic radius of the protein itself. That's why I can't simply filter the two to separate them.
Because the protein carries a significant surface charge, but the vitamin D particles are either uncharged, or significantly less charged, I thought I'd use an ion exchange column to trap the protein (and the vitamin bound to it), while allowing the uncharged vitamin to pass through.
However, when I tried running a sample including only vitamin D, I did not see the characteristic UV peaks that I saw when I ran the same sample through the system with no column attached.
Since the column contains PS and PE parts, I am guessing that my vitamin is getting stuck there. I'm wondering if I could find a system, maybe constructed of metal or glass, that would not cause this problem. I realize it's a little unusual to be looking for an ion-exchange column compatible with hydrophobic compounds, but that's what I'm looking for.
Because I don't want to disrupt the system, that rules out ACN.