Yes Whey Protein can be stored in a clear container if that's all you have although it's best to store the Whey Protein in a dark non see through container if you have one.
If you still have the whey protein in the original container it's best to store it in the original container sealed up and when you do store the whey protein the whey protein should be stored in a dry, cool place, such as a closet or pantry.
Make sure that it doesn't get humidity in the whey protein or it could cause it to get too hard and go bad.
Whey Protein will usually last a couple years before it goes bad.
Whey Protein does eventually go bad but it takes at least a couple years if not more before it does go bad.