Table VI

Patient RA2 (HLA-DRB1*0101/0401): Peptide sequences, source proteins and predicted binding registers of proteins associated with autoantibodies in RA patients

Peptide sequenceaNo. IDbGene nameSource proteinTEPITOPEc
01010401
SRLPIIDVAPLDVGAPD8COL1A1Collagen, type I, α-145
SLRPKDYEVDATLKSLNNQ15COL1A2Collagen, type I, α-21
QSGEYWIDPNQGSVE2COL5A2Collagen, type V, α-21
GDIQQFLITGDPKAAYD3COL11A1Collagen, type XI, α-174
SARLTWDPTSRQING1COL14A1Collagen, type XIV, α-12
VPPEWKALTDMPQMR4FGAFibrinogen α chain2
GSAGHWTSESSVSGSTG10FGAFibrinogen α chain73
LGEFVSETESRG2FGAFibrinogen α chain107
GETSEMYLIQPDSSVKPY1, 2FGBFibrinogen β chain42
QGGTYSKASTPNGYDN8FGGFibrinogen γ chain9
SPVTGYRVTTTPKNGPGPT5FN1Fibronectin61
DEPQYLDLPSTATSVN1FN1Fibronectin48
SKNTLYLQMNSLRAEDT15IGHV3Ig heavy chain variable11
YLQMNSLRVEDT2IGHV3Ig heavy chain variable11
YLQMNSVRAEDT2IGHV3Ig heavy chain variable11
AKNSLYLQMNSLRAEDT5IGHV3-11Ig heavy chain variable11
APRLLIYDASNRATG1IGKV3D-11Ig κ chain variable71
KHKVYACEVTHQGLS2IGKV1-5Ig κ chain variable2
TLQSFRQDVDNASLAR2VIMVimentin1
  • a Because the identified peptides varied in length, only the longest peptide is shown. Predicted P1 residues are bold for 0401 and underlined for 0101. Because multiple binding registers were predicted for many peptides, only the register with the highest likelihood of binding is indicated. For some peptides, a binding register to only one of the patient's HLA-DR molecules was predicted. Tandem MS/MS spectra obtained for the listed peptides are presented in supplemental material pages 56–74.

  • b Number of peptides identified in the patient's sample. Because of peptide length variability, not all peptides contained the predicted nine-amino acid core sequence for each HLA-DR molecule. Therefore, where the two numbers differed, 0401 is bold, and 0101 is underlined.

  • c The TEPITOPE binding score for the P1 site indicated.