The analysis of proteomic samples with affinity labels has been firmly established as a tool for the post-genomic researcher. Recent examples highlight the advantages of profiling functionally active members of specific protein families to identify therapeutically relevant protein targets that have escaped normal physiological regulation leading to increased or decreased activity. This dysregulation may result from any number of biological changes that modulate a protein's activity; for example, post-translational modifications of the protein or an imbalance between the protein and its endogenous inhibitor(s). By providing a direct measure of a protein's functional activity, affinity probe analysis identifies these changes and allows investigators to focus their research efforts upon those proteins that are most likely to be responsible for the biological changes under evaluation.