Table 1

Experimentally observed masses of PPI and IA-2 peptides eluted from highest-risk HLA-DQ2/8

EC50 (µmol/L)
Observed m/zCalculated m/zResiduesCorresponding protein sequenceDQ8transDQ8cis
PPI
Core 1
784.36783.3517–24WGPDPAAA0.3 ± 0.01nb
Core 2
600.641,798.9254–69TRREAEDLQVGQVELG16 ± 2 (26)64 ± 8 (26)
566.961,697.8755–69RREAEDLQVGQVELG
IA-2
Core 1
634.001,899.00142–159LQDIPTGSAPAAQHRLPQ17.7 ± 3.329.2 ± 5.9
591.311,770.94142–158LQDIPTGSAPAAQHRLP
Core 2
647.641,939.92293–311VPRLPEQGSSSRAEDSPEG13.0 ± 0.168.6 ± 44.5
580.781,159.55296–306LPEQGSSSRAE
638.291,274.57296–307LPEQGSSSRAED
681.811,361.61296–308LPEQGSSSRAEDS
794.851,587.70296–310LPEQGSSSRAEDSPE
823.361,644.72297–311LPEQGSSSRAEDSPEG
738.311,474.62297–310PEQGSSSRAEDSPE
766.831,531.65297–311PEQGSSSRAEDSPEG
718.291,434.59298–311EQGSSSRAEDSPEG
Core 3
508.581,522.74318–333GDRGEKPASPAVQPDA5.2 ± 0.657.6 ± 7.0
733.861,465.71319–333DRGEKPASPAVQPDA
489.571,465.72319–332DRGEKPASPAVQPD
451.231,350.69320–332RGEKPASPAVQPD
598.301,194.59321–332GEKPASPAVQPD
  • Alignments of naturally processed peptides derived from islet autoantigens presented by T1D high-risk HLA-DQ2/8. Residues in bold represent the anchor residues in the predicted minimal binding cores (MBR) of the naturally processed epitopes for HLA-DQ8trans and HLA-DQ8cis (MBR starting with R or K). Minimal 9 MBRs for HLA-DQ8cis/trans are underlined. HLA-DQ2cis/trans MBR were not predicted. Shown are the EC50 values of the longest eluted peptides from HLA-DQ8trans and -DQ8cis as validated by HLA-peptide binding studies. m/z, mass-to-charge ratio; nb, no binding.