PNGase F removes almost all types of N-linked (Asn-linked) glycosylation: high mannose, hybrid, bi-, tri- and tetra-antennary. You will choose this enzyme if your goal is to remove all N-linked carbohydrates without regard to type. Endo H removes only high mannose and some hybrid types of N-linked carbohydrates. You would choose this enzyme to more closely determine the type of N-linked glycosylation, or if you know that the protein has a carbohydrate sensitive to Endo H.