A multiple channel high throughput purification system for purifying a plurality of samples, preferably four or more samples from a chemical library. The high throughput purification uses chromatography, and more preferably, super critical fluid chromatography. Four parallel channels are provided in this system and coupled to a common analyzer and computer. The four channels direct the selected sample flow through a separator, such as an SFC column, a detector, such as a UV detector, to detect peaks within the sample flow, and a micro sample valve that splits a sampling of the flow to an analyzer, such as a mass spectrometer. The system also utilizes unique back pressure regulator assemblies and pressure relief assemblies to maintain a selected pressure within the purification channel. While the sample flow continues, the mass spectrometer simultaneously analyzes the sampling to determine if a target compound is within the sample portion. A fraction collection valve directs sample portions to one of two fraction collectors such as a microtiter plate. The purified target compounds are collected in one microtiter plate and the other non-desirable peaks are collected in a second microtiter plate in corresponding wells. In the supercritical fluid chromatography purification system, an expansion chamber is provided to condense the vaporous sample flow before the purified compounds are added to the particular well of the microtiter plate. A fraction collection assembly is used that automates the use of disposable expansion chambers for depositing the samples in the microtiter plates.