The discovery of targets that are sufficiently robust to yield marketable therapeutics is an enormous challenge. Through the years, several approaches have been used with varying degrees of success. These include target-independent screening of tumor-derived cell lines (disease-dependent), reductionist approaches to identifying crucial elements of disease-affected pathways, disease-independent screening of homologs of previously drugged targets, disease-dependent 'global' examination of gene transcript levels, and disease-dependent global examination of protein expression levels. These endeavors have been enabled by several major advancements in technology, most recently, the sequencing of the human genome. This review identifies the technical issues to be addressed for industrial-scale protein-based discovery in the identification of targets for therapeutic (or diagnostic) intervention. Such approaches aim to direct discovery in a way that increases the probability of robust target identification, and decreases the probability of failure owing to variable expression in this emerging field.