The VH clonotype, which represents a cluster of antibodies that likely originate from a single B-cell lineage (27, 28), is defined here as the group of VH sequences that share germ-line V and J segments and also exhibit greater than 90% amino acid identity in the complementarity-determining region (CDR)-H3 (threshold for CDR-H3 amino acid identity ...
For peptide identifications, a custom database of the antibody repertoire was built using high-quality V gene sequences from the peripheral B cells in each donor (Table S1),
Frequencies shown here were calculated by adding the CDR-H3 spectral counts for all peptides mapping to a single clonotype.
Direct observation of these LLPCs over the course of a vaccine response is extremely difficult in humans, because most LLPCs reside in the BM.
Importantly, in F(ab′)2 resulting from trypsin digestion of IgG, the presence of a conserved cleavage site (Arg) directly upstream of the CDR-H3 and at the fourth residue of the downstream CH1 constant region (Lys) consistently yields a peptide encompassing the highly informative CDR-H3 and the J region (Fig. S3).
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