Optimizing preparative LC/MS configurations and methods for parallel synthesis purification

Preparative LC/MS is widely employed to address the high-throughput purification demands of parallel synthesis. However, conflicting chromatography requirements and the complexities of applying MS-directed fractionation can limit its effectiveness in high-throughput parallel synthesis schemes. We report here an at-column dilution small-scale preparative LC configuration which satisfies the mass loading (>20 mg) and small fraction volume (<1.5 mL) requirements of discovery parallel synthesis schemes employing plate mapping. We also present a protocol for compound-specific optimization of the preparative gradient LC method and MS threshold for fractionation from a "prepreparative" LC/MS analysis of the crude material. We will demonstrate significantly improved preparative separations (relative to "universal" prep LC methods) and the selection of reliable and effective fraction threshold methods for diverse libraries. The methods and configurations are simple to implement and are equally suited for "open access" and "expert" applications of preparative LC/MS purification.