Biomolecular interaction analysis (BIA) which utilizes surface plasmon resonance (SPR) detection of affinity-captured analytes has been interfaced with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI). Femtomole quantities of a peptide, myotoxin a, were detected by direct MALDI analysis of sensor chips used during BIA of a polyclonal anti-myotoxin a IgG/myotoxin a system. Further, different interactive surfaces (flow cells) present on a single biosensor were targeted individually for mass spectrometric analysis. System compatibility of the combined approach was demonstrated with sensitivities, detection limits, and analytical performances comparable to those intrinsic to the individual analyses. The combined approach unites the real-time capabilities of SPR-based BIA with the qualitative specificity of mass spectrometry.