After recognizing an antigen, an antigen-presenting cell such as the macrophage or B lymphocyte engulfs it completely by a process called phagocytosis. The engulfed particle, along with some material surrounding it, forms the endocytic vesicle (the phagosome), which fuses with lysosomes. Within the lysosome, the antigen is broken down into smaller pieces called peptides by proteases (enzymes that degrade larger proteins). The individual  peptides are then complexed with major histocompatibility complex class II (MHC class II) molecules located in the lysosome – this method of "handling" the antigen is known as the exogenous or endocytic pathway of antigen processing in contrast to the endogenous or cytosolic pathway, which complexes the abnormal proteins produced within the cell (e.g. under the influence of a viral infection or in a tumor cell) with MHC class I molecules.
An alternate pathway of endocytic processing had also been demonstrated wherein certain proteins like fibrinogen and myoglobin can bind as a whole to MHC-II molecules after they are denatured and their disulfide bonds are reduced (breaking the bond by adding hydrogen atoms across it). The proteases then degrade the exposed regions of the protein-MHC II-complex.