Fig. 5: Only a small proportion of Ab-seq peptides overlap with the CDR3 region, and most BCR reference matches were from less expanded clonotypes in BCR-seq.
From: Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling
Peptides from digestion of serum Abs were analyzed by LC-MS/MS, and their sequences were aligned to references made from bulkBCR-seq and scBCR-seq data of the same individual. a Sample setup for Ab-seq. b Number of peptides identified by LC-MS/MS (All), aligned to reference BCR sequences (Ab-specific), and overlapping at least 3 aa with the reference sequence’s CDR3 (CDR3-overlapping). c Ab-seq peptide length in regard to the length of overlap with its reference’s CDRH/L3. d Number of CDR3-overlapping peptides by the sequencing method of the reference match: bulkBCR-seq, scBCR-seq, or both bulkBCR-seq and scBCR-seq (both). e Number of CDR3-overlapping peptides by protease treatment: AspN, Chymotrypsin (Ct), Chymotrypsin followed by Trypsin (Ct+Tryp), and Trypsin (Tryp). f Number of CDR3-overlapping peptides that mapped to only one reference clonotype or multiple clonotypes. g Number of uniquely mapped CDR3-overlappping peptides by clonal size ranking in descending order of the BCR-seq reference match in log10 scale.
