I'm trying to separate liposomes with bacteria encapsulated within them from "empty" liposomes. The main difference between them is the density and size so I figured that a gel column may work. Any ideas? Also can I somehow use HPLC?
If you want minimal damage to your bacteria, use gel permeation chromatography. You should use a proper gel (beads) based on the size / density of your particles (particle size cut off).
Ruysschaert, Tristan, et al. "Liposome retention in size exclusion chromatography." BMC biotechnology 5.1 (2005): 11.
Dimov, Nikolay, et al. "Formation and purification of tailored liposomes for drug delivery using a module-based micro continuous-flow system." Scientific reports 7.1 (2017): 12045.
I’ve separated lysosomes (actually trisosomes) after cell lysis based on density using ultracentrifugation. I think the reference I used was: The Journal of Biochemistry, Volume 87, Issue 1, January 1980, Pages 237–248. You'll need to test the density of your liposomes and adjust as needed.
I’ve never separated liposome using GPC. If they have bacteria in them they may be too large for GPC, but you wi need to check columns and if you find an appropriate column, test it for the ability to separate them. If you are collecting material, this is going to be very small scale.
HPLC separates based on affinity to the column packing (typical is hydrophobic). So unless surface of liposomes differ this will not work.
Field-flow fractionation (FFF) would be well suited to separate based on either size alone or size & density. It can separate from large macromolecules to 10’s of microns in size. Look at flow FFF (size) or sedimentation FFF (size & density). I'd start with flow-FFF.