sample preparation for mass spectrometry. 

Tools and reagents to extract, digest, enrich and

clean up proteins and peptides

Another approach that might work is ion exchange. Ion exchange columns or filters have high protein binding capacity. The proteins is eluted with salt or a change in pH. Whatever the colored material is, it will likely elute at a different condition than the protein, so the two can be separated. Afterwards, the protein can be buffer-exchanged against the desired storage medium.

Thanks Adam . i tried the graphite before but i was in a different country . just visiting a collaborative lab and couldnt find a quick supply. Your suggestion sounds quite good , I might have access to some ion exchange material instead.

Activated charcoal might also work for you.