Mass spectrometric approaches have recently gained increasing access to molecular immunology and several methods have been developed that enable detailed chemical structure identification of antigen֪antibody interactions. Selective proteolytic digestion and MS-peptide mapping (epitope excision) has been successfully employed for epitope identification of protein antigens. In addition, “affinity proteomics” using partial epitope excision has been developed as an approach with unprecedented selectivity for direct protein identification from biological material. The potential of these methods is illustrated by the elucidation of a β- amyloid plaque-specific epitope recognized by therapeutic antibodies from transgenic mouse models of Alzheimer’s disease. Using an immobilized antigen and antibody- proteolytic digestion and analysis by high resolution Fourier transform ion cyclotron resonance mass spectrometry has lead to a new approach for the identification of antibody paratope structures (paratope-excision; “parexprot”). In this method, high resolution MS-peptide data at the low ppm level are required for direct identification of paratopes using protein databases. Mass spectrometric epitope mapping and determination of “molecular antibody-recognition signatures” offer high potential, especially for the development of new molecular diagnostics and the evaluation of new vaccine lead structures.

Keywords: affinity mass spectrometry, proteolytic epitope excision, antibody paratope, Alzheimer´s Disease, FTICR-MS