Array systems that facilitate the simultaneous monitoring of many interactions between biological molecules and the analysis of cellular protein interactions with high throughput. The present invention provides methods and arrays for analyzing biochemical pathways by forming an array of immobilized biomolecules; exposing the array to biomolecules in solution; and detecting modification of the immobilized biomolecules, modification of the biomolecules in solution, and/or binding of biomolecules in solution to immobilized biomolecules.