Gentle release of the protein of interest from the staring material is a very important and delicate process. The protein of interest is often found inside the cells where it is produced and therefore cells have to be disrupted in order to release the protein of interest into solution. This process is known as cell lysis.
A description of traditional methods of cell lysis can be found here.
In this course we use the freeze-thaw method and sonication.
What is the drawback of the methods described to be gentler? You add enzymes and other substances to the protein you are trying to purify! Which is the opposite of purifying; however, sometimes it is avoidable as some very sensitive proteins cannot withstand the traditional methods.