Systems, methods, and apparatus provide integration of microscopic imaging and liquid chromatography-mass spectrometry on a microfluidic device. In one aspect, an apparatus includes a first wafer, a second wafer, and an emitter. The emitter is disposed between the first wafer and the second wafer. The first wafer defines a sample input hole. The first wafer and the second wafer define a first channel, the first channel including a first end and a second end. The first end of the first channel is proximate the sample input hole. The first channel is configured to contain separation media. The second end of the first channel is proximate the emitter.