John D Laycock and Thomas Hartmann

Abstract Automation is an essential component of industrialized processes, which need to be productive, efficient, and of high quality. The use of robotic liquid handling robots for high throughput sample preparation in 96-well plates has become commonplace in drug discovery laboratories utilizing mass spectrometry. However, potential bottleneck remain in the areas of sampling, formatting, and aliquoting prior to sample preparation. Also, data handling bottlenecks can exist at the data reporting and warehousing. The strategies for an integrated workflow from study request all the way to final data summary reporting are examined. The following areas of the process flow of mass spectrometry (MS) based analysis are discussed: sample handling & tracking, sample preparation, data acquisition, MS front-end automation, data analysis, reporting and visualization, data archiving and retrieving. The development and use of custom software for interfacing between commercial database systems, robotics, and automated LC/MS/MS systems is discussed.

Keywords automation, robotics; robotic liquid handling, scripting, Visual Basic, LIMS, XML, LC/MS/MS.

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