Glycans, which are one post-translational modification of proteins, are molecules with high structural heterogeneity which are formed by complex bonding of glucose, mannose, and other monosaccharides. It is known that their complex structure is related to regulation of protein functions, and various phenomenon can be observed depending on illness and other factors. These include abnormal glycan structures with the protein backbone and the absence of glycan bonding at sites where it is assumed that such bonding should occur. The information concerning complex glycan structures and the binding sites of glycan with the proteins is not coded directly in genes, but is created by the action of a large number of glycosyltransferases, which act in the protein biosynthesis process. Therefore, a direct analysis of the target glycoprotein is necessary in order to understand the structures and binding sites of glycans on glycoproteins. Although mass spectrometers are widely used in this type of analysis, almost all such analyses are performed with largescale, high performance instruments. This article reports a glycopeptide analysis using a Shimadzu MALDImini-1 compact MALDI-DIT mass spectrometer equipped with a digital ion trap (DIT), which is an original technology developed by our company.