A highly complex pool of Immunoglobulin G (IgG) antibodies circulates in plasma that play an important role in the defense against pathogenic bacteria. Such circulating IgG repertoires can contain a subset of protective IgG clones that contribute to a successful and sustained immune response. Simultaneously, other IgG clones may lead to a detrimental immune response, contributing to the dysregulation of the immune system observed in for example sepsis. So far, detailed characterization of the circulating IgG repertoire and its relevance for immunity against streptococci has remained elusive.
Here, we showcase a novel structural proteogenomics workflow to decipher the properties of circulating antibody repertories relating to immunity against bacteria and viruses. The workflow combines large-scale B cell receptor sequencing, state-of-the art quantitative mass spectrometry and de novo protein sequencing to quantify the circulating antibody repertoire and its glycan modifications in convalescent sera and in animals of infection. Furthermore, the method supports structural modelling of immune complexes using a combination of affinity-purification mass spectrometry, cross-linking mass spectrometry and structural modelling. Using these technical developments, we provide a time-resolved systems wide view of the maturation of the circulating antibody response and the targeted epitopes after immunization using the M1 protein from Streptococcus pyogenes. The work has also generated an extensive compendium of antibody sequences that can be recombinantly produced for further structural and functional characterization and to test potential protective effects in animal models of infection.