Prioritizing the proteome: identifying pharmaceutically relevant targets

Considerable attention is now being placed on prioritizing the proteome as the point of delivery for genomic information. Some of the challenges faced in prioritizing efforts from a pharmaceutical perspective, when presented with an incomplete proteome picture, are described. Examples of pharmaceutically relevant proteins are used to illustrate an informatics-based analysis of the proteome using knowledge of known drug targets. We show how results can be maximized by linking informatics approaches to experimental techniques and describe methods that can be used for prioritization within unprecedented protein families using, for example, single nucleotide polymorphism data and knowledge of disease pathways.