Ras is one of the guanosine triphosphate (GTP) binding proteins that plays a significant role in signaling events of cell growth and differentiation. It can exist in two states: guanosine diphosphate (GDP)-bound from (Ras.GDP; inactive) and GTP-bound form (Ras.GTP; active). This paper discusses the difference in tertiary structure between the active and inactive forms using the combination of chemical modification and mass spectrometry. This difference can be clearly recognized in the presence of a target protein. Raf-1 RBD (Raf-1 Ras-binding domain), as differing glycinamidation of carboxyl groups. It was possible to observe the difference between these two states using several hundred picomoles of sample. While it is true that it is difficult to obtain the whole picture of a protein by the combination of chemical modification and mass spectrometry, it is a promising approach for the characterization of surface structure using very small amounts of sample.