Do significant amount of proteins from cells find their way in supernatant during pelleting? If the answer is yes then I see two ways in which protein can be in the supernatant .
1) Through lysis during pelleting
2) Through leakage of protein from cells during pelleting
if significant amount of lysis occur during pelleting then obviously protein will be there in the supernatant due to lysis alone. However, If most cells (like 98%-99%) remain intact then only by leakage significant amount of protein can be in the supernatant. Both way can also contribute. Which is the case?