Top-down proteomics analysis revealed proteoform biomarkers for authenticating edible bird's nest

Edible bird's nest (EBN), a prized delicacy valued for its nutrition and commercial significance, is often counterfeited. Authenticating its origin and verifying genuine EBN in processed products is essential for food safety and consumer trust. This study optimized sample preparation for top-down proteomic analysis to identify proteoforms as biomarkers for EBN authentication. Acidic mammalian chitinase proteoforms were consistently detected across EBNs from different origins, indicating their potential as authenticity markers. Among tested methods, chloroform/methanol precipitation produced the most reproducible proteoform profiles for distinguishing geographical origins. Additionally, thermostable proteoforms were found in hot aqueous extracts and instant EBN soups, supporting their use in verifying genuine EBN in processed foods. Our approach introduces a top-down proteomic method for authenticating EBN in raw and processed products, offering a promising tool for combating food fraud and enhancing food safety. • AMCase proteoforms may serve as biomarkers to authenticate EBN from other foods. • EBN origins can be distinguished by proteoform profiles via top-down analysis. • Thermostable proteoforms help verify genuine EBN presence in instant soup.