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Raman spectroscopy is a highly informative technique that is routinely used to analyze the chemical bonds in molecules, such as peptides. However, while Raman spectra of aqueous single amino acids are well-characterized, proteins and peptides are usually found only in solutions in the presence of ions for stability or further analysis. The impact of ions on the Raman spectra of amino acids and subsequently on peptides and proteins has not been systematically studied. In this work, the impact of different metal ions on the Raman spectra of four significant amino acids (glutamate, tyrosine, cysteine, and serine) and N-methylacetamide (a model of a peptide bond) in aqueous solution was studied using density functional theory simulations and Raman spectroscopy experimental validation. The research focused on analyzing band shifts and variations in peak intensity when different cations commonly used in experiments (Li+, Na+, K+, Ag+, Au+, Cu+, and Cu2+) were present. Experimental evidence on Raman spectra variation of Glutamate in the presence of different concentrations of Cu2+is also provided. Our results show that the ions stay close to the oxygen atoms in the amino acids tested. With regard to Raman spectra, we show Cu2+promotes Raman resonance. We have characterized and tabulated the shifts in the characteristic Raman peaks of the amino acids in response to metal ions with the aim of providing a reference for interpreting Raman spectra of proteins and other biological materials.