I'm trying to isolate Lysosome using a percoll (sigma, cat# 4937) gradient of 57.6%, 43.2%, 28.8% and 20.2% (Ref: Lysosomal and non-lysosomal peptidyl hydrolases of the bloodstream forms of Trypanosoma brucei brucei; John D. LONSDALE-ECCLES and Dennis J. GRAB). I'm centrifuging the gradient at 25000 rpm for 35mins in a swing bucket rotor as mentioned in the paper. After the centrifugation I am taking 2ml of each fractions and diluting it 5X with the homogenization buffer and re-centrifuging it again at 20000rpm for 30mins. The problem is After centrifugation I am observing a percoll pellet along with the protein pellet. Because of the percoll pellet I'm facing problem in sample preparation for western blot. Please suggest me on what should I do so that I can get the lysosome enriched protein pellet from the fractions without pelleting the percoll.

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