Table 1.
Nested PAD4 Peptide Sets Identified by the Cell-Free MHC Class II Antigen Processing Systema
| intact PAD4 | GrB-cleaved PAD4 | cleaved/intact PAD4 | ||||
|---|---|---|---|---|---|---|
| peptide (residues) | PAD4 peptide sequence common core epitope |
total peptide peak area (ions × sec) |
# unique peptides |
total peptide peak area (ions × sec) |
# unique peptides |
fold-change in peptide peak area |
| MAQ(1−17) | MAQGTLIRVTPEQPTHA | 1.64 × 107 | 5 | 56.94 × 107 | 20 | 34.7 |
| ASP(44−61) | ASPGVVVDIAHSPPAKKK | 10.43 × 107 | 10 | 17.07 × 107 | 11 | 1.64 |
| LTM(78−93) | LTMKAASGSTGDQKVQ | 1.08 × 107 | 2 | 1.47 × 107 | 3 | 1.36 |
| ISY(94−105) | ISYYGPKTPPVK | 17.18 × 107 | 3 | 15.84 × 107 | 3 | 0.92 |
| IGY(354−368) | IGYIQAPHKTLPVVF | 0.21 × 107 | 1 | 8.27 × 107 | 4 | 39.4 |
| RGP(394−405) | RGPQTGGISGLD | 1.24 × 107 | 2 | 3.78 × 107 | 3 | 3.05 |
| QAL(445−461) | QALQDFLSAQQVQAPVK | 3.59 × 107 | 5 | 64.74 × 107 | 10 | 18.0 |
| VGH(468−488) | VGHVDEFLSFVPAPDRKG | 9.11 × 107 | 11 | 13.88 × 107 | 12 | 1.52 |
a
Rows 1 and 5−7 are PAD4 peptides who presentation was enhanced >3-fold by GrB cleavage.