Manipulating samples as droplets within microfluidic devices has emerged as an interesting approach for chemical analysis and screening. In segmented flow, one embodiment of this technology, nanoliter samples are manipulated in microfluidic channels as plugs separated by an immiscible fluid, such as air or fluorinated oil. These plugs serve as miniature test-tubes in which reactions can be performed at high throughput. Microfluidic tools have been developed to split, dilute, extract, and filter such plugs at rates up to 10 Hz. We have developed methods to analyze plug content by mass spectrometry (MS) and electrophoresis. A natural application of this technology is for high throughput screening. By coupling droplet manipulation with MS detection, it is possible to greatly reduce reagent consumption and eliminate the need for fluorescent labels or coupled reactions. The technology and application to screens of deacetylase reactions and protein-protein interactions will be presented. Droplet technology can also be used for chemical monitoring or sensing applications. In this approach samples emerging from a miniaturized sampling device are segmented for later analysis. We have used this method to monitor neurotransmitter dynamics in the brain. The technology and application to studies of neurotransmission in a Huntington’s disease models will be demonstrated.