XinPilot: a chemist-designed open‑source desktop workspace for traceable high-throughput synthesis and purity analysis

High-throughput chemistry enables parallel exploration of multiple reactions. But it often involves manual operations and the handling of data inputs and outputs across synthesis and analytical instruments that use different software and file formats. Automating high-throughput synthesis and purity analysis requires seamless information transfer throughout the process. Existing digital chemistry tools offer powerful capabilities for experiment design, automation, data management, and analysis; however, laboratories commonly rely on a combination of these tools rather than a single integrated platform. To streamline data transfer between the instruments used for synthesis (Tecan Liquid Handler), workup (Opentrons Liquid Handler), and purity analysis (Waters ACQUITY HPLC and QDa MS) at the Acceleration Consortium’s Medicinal Chemistry Self Driving Lab, we developed a workspace, XinPilot. XinPilot addresses this project-level interoperability problem through a chemist-designed Windows desktop workspace that brings together chemical stock information, synthesis records, reaction schemes, expected products, and analytical evidence within a portable project. Working alongside existing instrument-control systems, XinPilot generates worklists for the Tecan Fluent and Opentrons Flex and OT2 liquid handlers, records manual reagent additions, and imports transfer records from other liquid-handling workflows in Excel, CSV, and JSON-compatible formats. These results can be combined into a unified reaction map when they use the same plate format. Chemical IDs and reaction-to-analysis well mappings preserve the relationships among reaction compositions, expected products, and analytical samples. Integrated PyParse-based analysis allows chemists to inspect UV chromatograms, mass spectra, and integrated peaks. Chemists can also reassign product peaks for individual experiments while retaining the automated assignments for other experiments, without requiring coding knowledge. Experimental records, original imported files, and supported analytical inspection data can be retained in portable .xinpilot.zip projects for subsequent review, handover, and synthesis planning. An experimentally executed Suzuki–Miyaura campaign combining Tecan dispensing, manual additions, Opentrons aqueous workup and LC-MS review is presented as a tutorial-style demonstration of the workflow. Additional experimental examples independently performed by other chemists are provided in the Supporting Information. A separate demonstration uses published experimental data from 192 Chemspeed reactions. These data were converted into XinPilot-compatible transfer records and imported into two projects. Reaction structures were also generated using XinPilot's Cheminformatics tools, and both projects were exported as portable .xinpilot.zip files. Overall, XinPilot provides an integrated open‑source workspace for generating worklists for parallel synthesis and workup using Tecan and Opentron liquid handlers, facilitating the purity analysis and maintaining traceable links between experimental conditions, reaction products, and analytical results.