This invention presents the high throughput (HT) analysis technology for molecular fractions employing micro-array format. Molecules are fractionated according to the properties of molecules and are assigned primary designated orders while their tissue origins are assigned secondary designated orders such that each fractionated molecules become addressable and traceable. Fractionated molecules are recovered, arrayed, and analyzed according to the same primary designated orders and secondary designated order in a high throughput manner. The above properties of molecules can be measured and predicted.