Table 2

In silico binding predictions of natural islet peptides eluted from DQ6 expressed on DQ6/8 heterozygous DCs

Observed m/zCalculated m/zResiduesCorresponding protein sequence
PPI
 541.291,080.5614–22LALWGPDPA
 910.481,818.9514–23LALWGPDPAA
 784.36783.3514–24LALWGPDPAAA
 713.32712.3114–29LALWGPDPAAAFVNQH
IA-2
 Core 1
  620.341,239.67374–386NPGGVVNVGADIK
  666.681,998.03374–393NPGGVVNVGADIKKTMEGPV
 Core 2
  804.082,410.21491–513EILAEHVHMSSGSFINISVVGPA
  1,141.092,281.16492–513ILAEHVHMSSGSFINISVVGPA
  723.372,168.08493–513LAEHVHMSSGSFINISVVGPA
  685.672,055.00494–513AEHVHMSSGSFINISVVGPA
  661.991,983.96495–513EHVHMSSGSFINISVVGPA
  843.911,686.83496–511HVHMSSGSFINISVVG
  775.391,549.77497–511VHMSSGSFINISVVG
 Core 3
  1,028.572,056.13534–553AGLVKSELEAQTGLQILQTG
  1,239.672,478.33543–566AQTGLQILQTGVGQREEAAAVLPQ
 Core 4
  1,053.671,053.67582–593VALAGVAGLLVA
  • By using the peptide-binding motifs of protective DQ6 and susceptible DQ8, natural peptides derived from PPI and IA-2 eluted from autoantigen-pulsed DQ6/8-expressing DCs were in silico validated as DQ6-binding natural islet peptides (anchor residues in boldface type; minimal binding registers underlined). No prediction hits were observed for DQ8.

  • m/z, charge/mass ratio.