Probing Antibody-Antigen Interactions by Mass Spectrometry

Techniques that have been used for antigenic site mapping of linear epitopes in proteins include binding assays of protein components produced by synthetic chemistry (1 ,2 ) or by recombinant gene expression (3 ,4 ). More recently, epitope localization has been achieved through the use of synthetic and bacteriophage peptide libraries (5 –9 ). Although effective, these methods can be costly and time-consuming. A different approach to antigenic site mapping has been reported by Suckau (10 ), who compared the pattern of proteolytic digestion of free peptide antigen with the pattern produced from the antigen bound to an antibody. Alternatively, these workers subjected the peptide to proteolytic digestion and identified products that bound specifically to the immobilized antibody. In both cases, the peptides of interest were identified by ²⁵² Cf plasma desorption mass spectrometry. Recently, another approach, termed affinity-directed mass spectrometry (11 ) has been reported by us and others (12 –16 ) for probing antigen-antibody interactions.