Why did you discard the pellet and keep the supernatant in this step of the protein purification procedure?

I believe the pellet is discarded in this part of protein purification procedure because the pellet contains unwanted bacterial debris, these includes the bacterial cell walls, membranes, and chromosomal DNA. Additionally, the pellet contains little, if any, GFP and can be discarded. Protein purification is a procedure that is intended to isolate one or few proteins from a complex mixture, normally cells, tissues or whole organisms. The process is important for the purpose of characterization of the function, structure and interactions of the proteins of interest.