Multiplexing liquid chromatography (LC) systems, and synchronizing to a single tandem mass spectrometer (MS/MS), can generate the high throughput needed by maximizing the efficiency of the MS/MS detector. An integrated multiplexing system has been specifically designed to synchronize two LC systems and an SCIEX mass spectrometer, allowing injection of samples into two LC streams in parallel. The overlapping LC runs and efficient use of MS detection, achievable with the SCIEX MPX�-2 High Throughput system, is shown to result in an overall higher throughput for common routine analyses.