The successful integration of biospecific interaction analysis based on surface plasmon resonance and mass spectrometry produces a powerful technique that couples the benefits of sensitive affinity capture and characterization of binding events with the ability to characterize interacting molecules. A variety of biosensors has been used to capture proteins and peptides biospecifically on sensor surfaces, with subsequent analysis using mass spectrometry. Applying this type of analysis to proteomic studies could lead to ligand and protein-complex identification, and might provide clues leading to the identification of pathways.