Scenario-weighted decision framework for selecting cell-free protein synthesis reactor formats: a targeted literature dataset and multi-criteria analysis

Cell-free protein synthesis supports rapid prototyping, biomanufacturing, and portable diagnostics, but reactor-format selection is often based on local practice rather than explicit decision criteria. We developed a transparent workflow that combines a targeted literature search with explicit eligibility criteria, unit-standardized quantitative extraction, and scenario-weighted multi-criteria scoring to compare reactor formats across performance and deployment constraints. Fifteen studies met inclusion criteria and were grouped into batch (n=7), dialysis or continuous-exchange systems (n=4), microfluidic platforms (n=3), and hydrogel or compartmentalized systems (n=1, reported but not ranked). Yield values were normalized to ug/mL where possible and analyzed together with reaction time, complexity, scalability, and automation proxies. Batch and dialysis or continuous-exchange formats showed comparable median yields (600.0 and 608.5 ug/mL), while microfluidic systems were faster (median 5.83 h) but lower yielding (median 63.0 ug/mL). Under three locked scenarios (speed-first, yield-first, low-infrastructure-first), batch ranked first in all three; microfluidic formats ranked second only when time was prioritized, and dialysis or continuous-exchange ranked second, close behind batch, when yield was prioritized. Because the search was targeted rather than exhaustive, the dataset is a sample of the literature and the rankings are provisional. These results show that no single reactor format is universally optimal; rankings depend on scenario priorities. The framework provides a reproducible decision layer that can be updated as new studies are added. The attached archive contains the cleaned dataset, the analysis scripts, tables, figures and the PubMed result list of 30 September 2026.