Complete DNA pull-down LC-MS/MS protein identification list for porcine skeletal muscle enhancer study

This dataset contains the complete protein identification results from DNA pull-down coupled with LC-MS/MS experiments using breed-derived enhancer sequences (Duroc-enh1, Min pig-enh1, Duroc-enh2, Min pig-enh2) as probes against porcine skeletal muscle satellite cell nuclear extracts. The dataset includes 874 proteins identified after filtering contaminants, reverse-database hits, and unannotated entries. Each entry contains UniProt accession, protein description, gene symbol, sequence coverage, peptide counts, molecular weight, normalized abundance in Duroc and Min pig probe conditions, fold change, log2 fold change, and classification category (Duroc_enriched, Minpig_enriched, Duroc_only, Minpig_only, or No_difference). This dataset supports the findings reported in the manuscript "Multi-omics integration identifies a breed-divergent enhancer locus linked to transcription-factor recruitment, chromatin interactions, and muscle traits in pigs" submitted to Animal.