This dataset contains the proteomic profiles obtained by label-free quantitative mass spectrometry (LFQ-MS/MS) comparing protein expression in wild-type (WT) Staphylococcus xylosus and its mutant strains ΔnrdR and Δrex. Each bacterial strain was cultured independently with three biological replicates. Protein extraction, trypsin digestion, and LC-MS/MS analysis were performed to identify differentially expressed proteins. The data elucidates molecular differences associated with the deletion of transcriptional regulators nrdR and rex, revealing key proteins involved in bacterial persistence and adaptation.