The typical method is to precipitate the proteins using 0.1% TCA in 10% ethanol aqueous solution (kept ice cold). You can set this on ice for 30 min before centrifuging the proteins. What remains in solution are the small molecules. Depending on the sample concentration, you can promote protein and nucleic acid precipitation by adding some BSA to the sample to create a bigger pellet.

Check https://www.mdpi.com/2218-1989/7/4/53/pdf

Check on this paper

https://www.mdpi.com/2218-1989/7/3/43/pdf