A: For the purposes of menu transcription, protein refers to meat.

Cheese is technically protein but it should be recorded as a topping addition, not under protein choices.

Below is an example of when a non-meat might be included in a list of protein choices.
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Item: Rice Bowl
​Description: Choose your protein
​Modifiers: Protein Choice

Vegetables can also have protein in them so the customer must make the choice of where they want their protein to come from (a meat or a vegetable). 

The same applies if the modifier list is like so:

Item: Rice Bowl
​Description: Choose your protein
​Modifiers: Protein Choice