A novel boronic acid functionalized mesoporous silica, which holds the attractive features of high surface area and large accessible porosity, was developed to enrich glycopeptides. This is the first time that mesoporous material has been introduced into glycoproteome. In comparison to direct (traditional) analysis, this novel method enabled 2 orders of magnitude improvement in the detection limit of glycopeptides. The unbiased nature of organo-boronic acid groups also made this method applicable to all kinds of glycopeptides regardless of their sizes, structures, and hydrophilicities.