Abstract: Collagen is the main constituent of gelatinous Chinese medicine, with deer hide gelatin (Cervi Corii Colla, DHG) made from deer hide (DH) through a complex thermal and high-pressure processing procedure. During this procedure some amino acids in collagen undergo hydroxylation and deamidation. In the present study, comparative analysis of proteins and peptides in DH and DHG was carried out using "peptidomics-modifications" methods. Nano-LC-MS/MS was used to analyze proteins and peptides in DH and DHG, and the number and sites of modification were determined as well. The amount of hydroxylation and deamidation that occurred in DHG was significantly greater than that in DH, suggesting that under thermal and high-pressure processing these modifications occurred more frequently on certain amino acids in collagen, and might be correlated with hydrophobicity. The occurrence and mechanism of hydroxylation and deamidation in DH processing procedures should be explored in further research. The present study provides important evidence of the chemical constituents and the correlation of processing procedures with these modifications, and also suggests some investigative ideas for DHG processing optimization and improvement of quality standards.