Systems and methods for analyzing a plurality of samples in parallel include a plurality of liquid phase separation regions, a plurality of microfluidic storage regions, and a common mass spectrometer. Samples are separated in parallel in the separation regions to yield a plurality of output streams that are stored in the storage regions. The contents of each storage region, or at least a representative portion thereof, are sequentially discharged, ionized, and directed to the inlet of a mass spectrometer. In this manner, multiple separations are conducted in parallel with outputs provided serially to a common mass spectrometer without any loss of data. Microfluidic storage regions minimize diffusion between bands of separated samples. Portions of separated samples may be directed to fraction collectors.