Devices and processes for synthesizing, purifying and analyzing large numbers of compounds for use in combinatorial libraries, are disclosed. The processes involve generating a series of compounds in multi-well plates or multi-tube racks, purifying the reaction mixtures, analyzing the purified compounds, and optionally performing bioassays on the compounds. The information regarding the compounds is stored in a central database. The devices include one or more multi-tube configurations, a purification device, means for transferring the contents of the tubes, a solvent evaporator, analytical instrumentation, and, optionally a weighing instrument. The multi-tube configuration(s) optionally include a cover, which can be placed on or removed from the configuration by computer control. By correlating the orientation of tubes from one stage to the next, it is possible to use a single bar code or other identifying mark for each multi-tube configuration rather than for each individual tube. This simplifies data collection for large numbers of compounds. An interface also described herein permits one to use racks from one vendor and other components from other vendors.