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A novel approach based on molecularly imprinted polymer (MIP) was developed to improve the extraction capacity of lysine acetylation peptide in real sample. Green deep eutectic solvents (DESs) were introduced and used as one of synergistic functional monomers with zinc acrylate (ZnA). Glycine-glycine-alanine-lysine(ac)-arginine (GGAKacR) was chosen as template, and N, N'-methylenbisacrylamide (MBAA) was used as cross-linker. The obtained GGAKacR-MIP had excellent selectivity for the template with imprinting factor up to 21.4.