Analysis of biomolecular interaction epitopes has recently become a key step in the development and molecular evaluation of therapeutic antibodies, biomedical peptide and protein biomarkers and molecular vaccines. Bioaffinity analysis using biosensors has become an established technique for detection and quantification of biomolecular interactions. However, a principal limitation of biosensors is their lack of providing chemical structure information of affinity-bound ligands. Proteolytic excision/extraction (PROTEX-MS), hydrogen-deuterium exchange (HDX-MS) of peptide backbone hydrogens, and Fast-Photochemical Oxidation (FPOP) are major techniques for mass spectrometry-based elucidation of protein-ligand interactions, but none of these tools alone provide quantitative affinity data. Using a surface plasmon resonance (SPR) biosensor, we have developed a continuous online biosensor-MS combination with electrospray ionization mass spectrometry that enables the simultaneous affinity isolation, structure identification and affinity quantification of biopolymer ligands from a protein-ligand complex immobilized on a gold chip.