The phenol concentration is too high for the modified Lowry assay (for proteins) to be reliable. I've found that in most methods phenol in some way interferes in one of the reactions and selectively removing the phenol (or the proteins) seems like a tricky task as well.
Refractive index can be a good parameter for protein and carbohydrate concentration measurements.
SEC-MALS or FFF-MALS with UV-LS-RI detection. The RI detector will measure the concentration of your protein & carbohydrate, while the UV detector will measure only the concentration of your protein. Subtracting the UV concentration from the RI concentration will leave you with the amount of carbohydrate present.
To do this, you will need 3 parameters:
1. dn/dc of your protein (most likely 0.185 ml/g)
2. dn/dc of the carbohydrate (typically in a range of 0.135 - 0.145 ml/g)
3. UV extinction coefficient of your protein at 280 nm (varies by protein)
Wyatt Technology's Astra 6 software does this calculation nicely for you: http://www.wyatt.com/solutions/properties/conjugation-proteins-membrane-proteins-copolymers.html
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