How can I help my dog get over being afraid of storms?

I have a English Springer Spaniel that's a little over 2 years old. I rescued him from the pound about 1 and 7 months ago. He is really afraid of big noises and storms, he was originally from a puppy mill, and brought to the pound when he was 3 months old. There''s only two reasons I can think of why he is afraid of storms 1) He was left outside during them at the puppy mill or 2)Our humane society/Pound have a metal sheet roof so it's probably noisy when it rains and storms. How can I help Puppy get over being afraid of storms?