Novel approach to optimization of a high-throughput semipreparative LC/MS system.

Automated semipreparative LC/MS systems are now well established commercially and commonly used for purification of early stage drug discovery compounds. A number of vendors have instruments on the market that are capable of reliably purifying compounds with good water/acetonitrile solubility. However, these systems often fail when the sample has poor solubility, extreme polarity, and/or poor ionization. Even in cases when substantial optimization has been done prior to purification, a certain percent of failures to recover the desired product is unavoidable. In the past, when the majority of samples run on LC/MS semipreparative systems were large combinatorial libraries, some losses in this high throughput mode were acceptable. However, now that more chemistry laboratories are making smaller more focused libraries with higher purity requirements, reliability and recovery are more crucial. This paper describes modifications made to customize an MS-triggered semipreparative LC/MS system in order to ensure improved reliability and recovery of products from traditional medicinal chemistry as well as combinatorial libraries.