An approach to customizing the data acquisition and interpretation process of liquid chromatography electrospray mass spectrometry (LC-MS) analysis of compound libraries is presented. Macro programs, using Microsoft Visual Basic, were applied to allow the seamless flow of data from the sample synthesis stage through data acquisition/interpretation and reporting, with minimum user interaction. Logical functions were also incorporated into the macros to allow automated actions to be performed based on experimental results. The application of this approach as a universal method for supplementing the automation process of other instruments controlled by the Microsoft Windows PC platform is also discussed.