Synthetic peptides are becoming increasingly important in industry and academia, including applications in peptide-based therapeutics. While Solid Phase Peptide Peptide Synthesis (SPPS) is largely automated, current software options for describing this process are instrument-specific, with no unifying standard protocol specification. Post-synthesis modification of peptides in the solution phase is also performed manually. As a result, discovery and process optimization remains an iterative and manual process, requiring large amounts of human intervention and labor.

Here we introduce TideScript: a domain specific language for peptide chemistry. TideScript aims to provide a programming language to standardize protocol descriptions, allowing unambiguous specification, increased automation, and autonomous optimization. At present, TideScript is a formal specification language, with scope to expand into full execution on hardware.

We give a full description of TideScript, including its syntax and a small-step operational semantics, and show how TideScript can encode three common peptide protocols: peptide chain assembly by SPPS, peptide cleavage and thiol-malemide conjugation. We compare this approach to existing non-peptide-specific chemical protocol languages, χDL and BioScript.