Peptide mass fingerpringting spectra of south buffalo milk casein and soybean protein were established byusing a LTQ Orbitrap XL mass spectrometer combined with RP- HPLC techniques,and the corresponding aminoacid sequences were compared.The results indicate that,among the 28 detected peptides fractions obtained by thetryptic hydrolysis of α_s1 - CN,β- CN and κ- CN originated from south buffalo milk caseins,no fraction matches withthe 181 peptides fractions from the glycinin (glycinin G1 ～ G5 subunit) and the β- conglycinin (α,α',β subunit) ofsoybean protein components,Moreover,it is found that there exists great differences in the number,composition ra-tio and arrangement patterns of amino acid subunits between south buffalo milk caseins and soybean protein compo-nents,and that the full amino acid sequence of soy protein subunits is longer than that of casein amino acid compo-nents,the molecular mass of each component of soy protein is significantly higher than that of the components of ca-sein.The adopted LTQ Orbitrap XL mass spectrometry technique for analyzing the peptide mass fingerprint of milk-derived protein provides a high- precision tool for identifying cheap proteins in milk protein and lays a reliable theo-retical foundation for the detection of trace components in complex mixture.