Abstract: Deamidation is one of the most common degradation impurities in protein and peptide drugs. The deamidation of glutamine and asparagine in the protein sequence can lead to changes in the chemical and biological properties of the protein. However, the rutine trypsin-based pretreatment process can significantly increase the artificial deamidation impurities during the digestion process, resulting in high determination level. In this study, after optimizing the conditions of Glu-C enzymatic hydrolysis, we obtained the best enzymatic conditions under acidic condition and the artificial deamidation impurities significantly reduced in digestion process, identified the deamidation site (N48). Through the methodological investigation and comparison of the measurement results of different methods, the specificity, reproducibility and accuracy of the method are verified. The method established in this research has laid a solid foundation for the accurate determination of deamidation impurities in cobratide and its similar protein peptide biochemical drugs.