cjs-202301-0005 ArticleInAPeriodical 2023 Czech Journal of Animal Science 68 1 17-29 ZhangChongyan XieYuchun GuoJuntao SuXin ZhaoCun QinQing DaiDongliang WangZhixin LiJinquan LiuZhihong Label-free proteomics to identify keratins and keratin-associated proteins and their effects on the fleece traits of Inner Mongolia Cashmere Goats Inner Mongolia Cashmere Goat fleece is derived from a heterogeneous coat. The guard hair is produced by primary hair follicles, and the down hair is produced by secondary hair follicles. Reports have focused on research related to the different hair follicle types, but no related study has addressed the difference in the proteins of down hair (DH) and guard hair (GH), and whether the protein composition of these materials differs remains to be studied. The protein composition of DH and GH was studied. A total of 108 proteins were identified in DH, and 116 proteins were identified in GH; 39 proteins were differentially expressed, of which 18 proteins were upregulated and 21 proteins were downregulated in DH versus GH. In this study, through the measurement of DH and GH samples from Inner Mongolia Cashmere Goats, the diameter of DH relative to GH was downregulated (P < 0.05), a property that may be related to the KRT38 protein. Moreover, the strength of GH was significantly higher than that of DH (P < 0.05), a property that may be affected by the KRTAP8-1 protein. GO analysis showed that the different traits of DH and GH from Inner Mongolia Cashmere Goats are affected by keratin, actin, and calcium-binding proteins. This study uses a nonlabelled quantitative proteomics method to study the proteins in DH and GH, aiming to identify the keratin family in Inner Mongolia Cashmere Goats and to provide a new direction for studying DH and GH traits at the protein level.