Data from: A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes

Antibodies are essential to functional immunity, yet the epitopes targeted
by antibody repertoires remain largely uncharacterized. To aid in
characterization, we developed a generalizable strategy to identify
antibody-binding epitopes within individual proteins and entire proteomes.
Specifically, we selected antibody-binding peptides for 273 distinct sera
out of a random library and identified the peptides using next-generation
sequencing. To identify antibody-binding epitopes and the antigens from
which these epitopes were derived, we tiled the sequences of candidate
antigens into short overlapping subsequences of length k (k-mers). We used
the enrichment over background of these k-mers in the antibody-binding
peptide dataset to identify antibody-binding epitopes. As a positive
control, we used this approach, termed K-mer Tiling of Protein Epitopes
(K-TOPE), to identify epitopes targeted by monoclonal and polyclonal
antibodies of well-characterized specificity, accurately recovering their
known epitopes. K-TOPE characterized a commonly targeted antigen from
Rhinovirus A, identifying three epitopes recognized by antibodies present
in 83% of sera (n = 250). An analysis of 2,908 proteins from 400 viral
taxa that infect humans revealed seven enterovirus epitopes and five
Epstein-Barr virus epitopes recognized by >30% of specimens.
Analysis of Staphylococcus and Streptococcus proteomes similarly revealed
six epitopes recognized by >40% of specimens. These common viral
and bacterial epitopes exhibited excellent agreement with previously
mapped epitopes. Additionally, we identified 30 HSV2-specific epitopes
that were 100% specific against HSV1 in novel and previously reported
antigens. The K-TOPE approach thus provides a powerful new tool to
elucidate the organisms, antigens, and epitopes targeted by human antibody
repertoires.