Peptide barcoding: an alternative to the phenotype-genotype problem

Barcoding methods are powerful tools for screening large libraries and have successfully been employed using DNA-centric approaches for over two decades. Yet despite the central role of proteins in most biological processes, protein-based barcoding methods have only recently emerged as a viable alternative. In this review we summarize recent advances in peptide barcoding and highlight its diverse applications, including screening of binding affinity, lipid nanoparticles, mRNA untranslated regions, and designed protein libraries. We discuss key challenges in barcode design, library construction, and mass spectrometry methods for accurate, scalable, and high-throughput screening. We propose that peptide barcoding represents a conceptual shift in genotype-phenotype mapping and will play an increasingly important role in AI-driven protein engineering, delivery technologies, and synthetic biology.