Simultaneous measurement of molecules from many samples is particularly useful for screening of certain molecules from different samples, for targeting verification of results obtained from protein and cDNA arrays, and for molecular epidemiology-based investigations. Described herein is a sensitive and quantitative approach, referred to as enhanced protein profiling arrays, that measures molecular expression levels from numerous samples. Enhanced protein profiling arrays can easily be constructed from tissue lysates, cell lysates, conditioned media, and body fluids, along with standard proteins and appropriate controls onto antibody-coated surfaces of solid supports. Coupled with many common detection techniques, the expression levels of certain molecules can be determined quantitatively. An account of the successful development and application of this enhanced protein profiling array technology is presented.