What I think is centrifuge filtration would it be a good test for encapsulation efficiency.
You will need to know, from an averaged sample, contents entrapped and estimate that by HPLC/spectrophotometrically depending upon certain criteria of your material and formulation.!
You can perform HPLC/UV after an accurate sample preparation. If you have liposomes, after disruption.
Dialysis method can be applicable if the formulations are nano size. Bioactive agents loaded particles were dialyzed to eliminate free drug. Perform suitable spectroscopic method (UV/HPLC) to quantify the encapsulated drug.
You can use either the direct method which is this one (what is encapsulated into the particles) or the indirect (what was not encapsulated into the nanoparticles) in order to calculate the encapsulation efficiency. in the first method as you nicely describe you will have to dissolve the nanoparticles and the encapsulated drug (nanoformulation) in the same solvent and measure the concentration of the drug with any analytical method suits you best. With the indirect method you can measure the drug that was not encapsulated (measure the supernatant after the procedure of encapsulation and the isolation of the nanoparticles (centrifugation). Please check also if you like the papers mentioned bellow
How do I calculate encapsulation efficiency? - ResearchGate. Available from: https://www.researchgate.net/post/How_do_I_calculate_encapsulation_efficiency [accessed Oct 16, 2016].
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