S1)

S1). of the antigen-specific CDRH3 peptide mass spectral counts. For assessment, antibodies with 18 different CDRH3s (12 clonotypes) were displayed in the antigen-specific IgG portion from an unimmunized rabbit that fortuitously displayed a moderate titer for BSA. Proteomically recognized antibodies were synthesized and shown to display subnanomolar affinities. The ability to deconvolute the polyclonal serum response is likely to be of important Deramciclane importance for analyzing antibody reactions after vaccination and for more completely understanding adaptive immune responses in health and disease. = 4729 VH genes, blue bars), peripheral B cells (= 2788 VH genes, reddish bars), or from antibody proteins recognized by proteomic analysis of the serum affinity purified IgGs (= 334, green bars) for the CCH rabbit. To generate antibodies, proteomically recognized VH sequences must be Deramciclane combined with the VL genes. We consequently synthesized VH website DNAs and used these to construct phage displayed scFv libraries comprising the VL cDNA repertoire. Functional scFv antibodies were isolated after two to three rounds of phage panning. Putative pairings of VH and VL genes were then indicated recombinantly as full-size IgGs in mammalian cells and isolated to characterize their antigen affinity and features. V Gene Repertoire Analysis. Preliminary studies in mice exposed that the strategy explained in Fig. 1 was able to successfully determine abundant, antigen-specific IgGs in the serum of immunized mice. However, the small amount of serum that is from mice at killing (0.8C1.5 mL) resulted in low counts of V-gene informative peptides and poor MS recognition statistics. Larger amounts of serum can easily become from humans, as well as other comparatively larger animals such as rabbits, an Deramciclane animal model that has been used extensively for immunological studies for nearly a century. For the present study, a New Zealand white rabbit (hemocyanin (CCH) in total Freunds adjuvant (CFA), boosted with antigen in incomplete FA and killed 1 wk after the final boost (CCH rabbit). Additionally, to further validate our approach we performed serum IgG deconvolution on an unimmunized rabbit that, remarkably, was found to exhibit a titer toward BSA (BSA rabbit; this observation occurred fortuitously because BSA was used as the common blocking agent in our ELISA protocol). Unlike the BSA rabbit, the animal immunized with CCH did not show any titer toward BSA. We prepared RNA samples from total peripheral B cells (PBCs), total bone marrow cells, and CD138+ bone marrow plasma cells (BM-PCs) Rtp3 isolated by magnetic sorting. First-strand cDNAs were generated using an oligo(dT) primer, and double-stranded products were amplified via 5 RACE (16) using primers complementary to rabbit IgG CH1 ( 2 reads. Consistent with earlier reports of limited germ-line V gene diversity in rabbits (19, 20), we found that 89% of the VH genes in the IgG repertoire (CCH rabbit) were derived from only two germ-line V genes (1S40 and 1S45), and an mind-boggling 75% contained the IGHJ4 section. V gene and J gene use was highly related in BM-PCs and PBCs. In the BSA rabbit, 86% of the VH sequences were derived from 1S44, 1S45, and 1S40, whereas 55% contained the IGHJ4 and 28% contained the IGHJ2 J-segment (analysis of the V gene database showed that digestion with trypsin should generate peptide fragments with plenty of coverage of the CDRH3 region and of lengths appropriate for MS detection to uniquely determine 91.4% of the putative antibody clones ( 2 reads) concatenated with the rabbit full protein-coding sequence database (OryCun2) and MaxQuant contaminants database (23, 24). Postsearch processing from the Percolator algorithm (25) generated a dataset of peptide-spectrum matches (PSMs) with an expected false-discovery rate <1%. False identifications were further controlled.