Comparative analysis of caseins in Saanen goat milk from 3 different regions of China using quantitative proteomics

A quantitative proteomic technique based on data-independent acquisition (DIA) was used to analyze differentially expressed caseins of Saanen goat milk samples collected from 3 regions in China (Guangdong, GD; Inner Mongolia, IM; Shaanxi, SX). A total of 345 proteins were quantified in each sample. Gene Ontology (GO) analysis showed that proteins were mainly involved in cellular process and cell and binding functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that proteins were mainly involved in metabolic pathways. Differentially expressed proteins (DEP) between goat milk from 3 comparison groups composed of paired regions were compared and analyzed. The number of DEP was 114, 69, and 79 for GD versus IM, GD versus SX, and IM versus SX, respectively. The GO enrichment analysis of the 3 comparison groups showed that differences were mainly related to the regulation of biological quality, biological regulation, and response to stimulus in terms of biological process; extracellular region for cellular component; and binding function for molecular function. Pathways in which DEP of GD versus IM, GD versus SX, and IM versus SX were mostly protein processing in endoplasmic reticulum for the first 2 groups and metabolic pathways for the last. Protein-protein interaction network analysis demonstrated that the most prominent DEP was heat shock protein 90 β family member 1 for both the GD versus IM and the GD versus SX groups, and haptoglobin for the IM versus SX group. Data from this study may offer useful information for further investigation of the protein composition of Saanen goat milk and its application in the dairy industry.