Characterization and discrimination of Tibetan and Duroc × (Landrace × Yorkshire) pork using label-free quantitative proteomics analysis

Abstract The primary aim of this study was to unravel key proteins for the differentiation of Tibetan ( n  = 15) and Duroc × (Landrace × Yorkshire) (n = 15) pork. A platform consisting of LC-MS/MS analysis and label-free quantitative proteomics was utilized. Changes in the proteome profiles were observed for different pork cuts. A total of 91 and 116 differentially expressed proteins (fold change >2 or  p -value n  = 54) and 47.1% ( n  = 48) were up- and downregulated, respectively, in DLY pork compared to TP. Functional analysis of these proteins revealed that the most significantly enriched gene ontology term for the biological process was the purine-containing compound metabolic process ( p  = .003), while that with respect to molecular function was threonine-type peptidase activity ( p  = .002) and that for the cellular component was the mitochondrial inner membrane ( p  = .001). The most significantly enriched KEGG pathway was involved in histidine metabolism ( p  = .01), followed by oxidative phosphorylation ( p  = .02). Proteins involved in oxidative phosphorylation were overabundant in TP. Using a chemometrics approach, we identified 68 significant proteins for the discrimination of TP and DLY pork. The most significantly upregulated proteins in TP and DLY pork were nicotinamide nucleotide transhydrogenase and heat shock protein 90-beta, respectively. This study demonstrates the feasibility of using differential proteomic analysis to discriminate between TP and DLY pork, and the current dataset can be expanded to a larger sample size for possible discriminant validation.