Amino-functionalized macroporous silica (NH2 -MOSF) has been developed as a host reactor to realize highly efficient proteolysis in acidic solutions where normal tryptic reactions cannot occur. The digestion protocol consists simply of adding the functionalized NH2 -MOSF into the protein and trypsin solutions without altering the bulk pH or pre-loading the enzymes on the materials. With this protocol, digestion of sample fractions from liquid chromatography (LC) can be efficiently realized in the acidic solutions directly. Digestion of a protein fraction extracted from rat liver tissue after LC separation was performed to illustrate this principle, where 103 proteins were successfully identified at pH 3 after 1.5 hours of tryptic digestion.