Advances in biomolecular mass spectrometry (Bio-MS) have made this technique an invaluable tool for analytical chemists and biochemists alike. The applicability of Bio-MS approaches in drug discovery now encompasses in vitro, cellular, and in vivo pharmacological and clinical applications in an unprecedented expansion of utility. As a result, the role of Bio-MS in pharmaceutical discovery continues to proliferate for both structural and functional characterization of biomolecules. From target characterization to lead optimization, affinity techniques have been used to purify, probe, and enrich analytes of interest. Affinity selection employed prior to MS analysis can "edit" out extraneous noise and enable the researcher to examine only what is important. These affinity-based methods can be used as an alternative strategy when classical biochemical techniques are insufficient in advancing difficult projects. We have applied various affinity techniques in conjunction with mass spectrometry throughout the drug discovery process. This perspective will describe affinity-based mass spectrometry methodologies and related concepts, illustrated with original results.