A freeze dryer includes a chamber, a vacuum pump, a cooling system, a heating system, and an electronic controller, which can include a display device. The electronic controller includes a drying process. The drying process includes heating a material in the chamber at or near ambient pressure while simultaneously cooling at least one interior wall of the chamber. In some embodiments, the controller can display options, such as options to heat the material, and receive user input. In some embodiments, the material can be heated to at least 90 F.

Certain aspects provide methods of producing a high protein confection, comprising the steps: (a) mixing wet ingredients, dry ingredients and a protein ingredient in a cooking chamber to form a raw confection, wherein the cooking chamber is at a temperature of about 35 C. to about 60 C., and (b) applying a vacuum to the cooking chamber to about 15 in. Hg to about 29 in. Hg while continuing to mix the raw confection to form a finished confection. Certain aspects provide a high protein confection made by these methods.