BACKGROUND: Peptides are compounds formed by the dehydration-condensation reaction of two or more amino acids which play an important role in the life functions of the organism. Changes in the structure of amino acids and peptides are vital for elucidating the process of disease development. However, the existing methods make it difficult to accurately recognize slight variations in peptide sequences, which becomes a difficult detection task. Therefore, the necessity of novel, accurate, comprehensive and deep strategies for peptide sequence identification is imperative. RESULTS: Here, an intelligent decoding system was developed, which synthesized a substrate (Ag/BD SIGNIFICANCE: In sum, the original, versatile and intelligent detection system based on surface-enhanced Raman scattering we proposed provides a promising method and strategy for the precise and valid analysis of different variations of peptide sequences, which is of great significance for explaining life processes, exploring disease pathogenesis, and developing innovative drugs.