This study took the advantage of the availability of a methylated mutant (ΔpglX ) of Lacticaseibacillus (L.) paracasei Zhang to test our hypothesis that DNA methylation could protect lactic acid bacteria from freeze-drying and post-freeze-drying storage stresses. Active cultures of the wild-type and mutant were freeze-dried and stored at 30 ℃ for different duration (30, 60, and 90 days) before reactivation. Proteomic analyses was implemented to identify differentially expressed proteins (DEPs) of the bacteria.