I thought proteins were broken down by pepsin?

There are many different enzymes that are proteases; that is, they can break down protein.  Pepsinogen is the inactive form of a protease enzyme that is released into the stomach.  It is broken down to the active form, pepsin, by the HCl (hydrochloric acid) also produced by the stomach.  

There are other proteases produced by the pancreas, and released into the small intestine, also to break down proteins; trypsin is one of them.  (Originally produced in the form of trypsinogen, the inactive form, and converted to the active form in the duodenum - the very first part of the small intestine).

There are many enzymes that break down proteins. Pepsin is a digestive enzyme in the stomach which is produced when a precursor protein, pepsinogen, is activated by hydrochloric acid in the stomach. Trypsin is another kind of enzyme for breaking down proteins. It is secreted by the pancreas as trypsinogen and is activated by another enzyme in the small intestine.