The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) in concert with surface plasmon resonance-based biomolecular interaction analysis (SPR-BIA) is reported. A chip-based biosensor unit was used to simultaneously monitor biomolecular interactions taking place on four different regions of the sensor chip (flow cells). Species retained during SPR-BIA were then identified by performing MALDI-TOF directly from within the area of the flow cells. Analyses were performed on an antibody/antigen/antibody system with detection limits in the low-femtomole range. The combined assay demonstrates the use of SPR-BIA to evaluate the relative stability of sequential solution-phase interactions, as well as, upon MALDI-TOF analysis, the ability to unambiguously confirm the presence of species retained during the interaction analysis.