If you are working at a small scale you could use 3k spin filters to remove all large proteins. Obviously small peptides would still pass through the membrane.

Physical methods are efficient. Protein depletion plates, SPE cartridges, and membranes also exist. I strongly recommend iphree phospholipid and protein removal resins from Phenomenex. In the case of unavailability, you may treat your sample with proteinase K to convert proteins into their corresponding peptide mixtures. Proteinase K will auto-digest itself in time...Both ways are versatile for the metabolomic approach excluding the lipidomic investigation...Simple ACN-acetone precipitation may also deplete the protein content depending on your experiment target.

Dear Sir you may try the protein separation with foam fractionation coloumn. it would suppose to help you