Table VII

Identification of S-cysteinylated peptides

The mass spectra from each patient's sample were searched for the potential post-translational modifications of O-N-acetyglucosamine, acetylation, amidation, citrullination, cysteinylation, S-cysteinylglycine, S-glutathionylation, S-glycation, S-homocysteinylation, 4-hydroxy-5-nonenal, malondialdehyde, methylation, oxidation, and phosphorylation. Tandem MS/MS spectra obtained for the listed peptides are presented in supplemental material pages 75–84. For search parameters and detailed results on cysteinylated peptides, see supplemental Excel Files E2 and E3.

Peptide sequenceaNo. of peptidesSource proteinTEPITOPEb
RA2LA1RA2LA1 1101
01010401
LKTGKLVSLSAQNLVDCCys33Cathepsin S157
KTGKLVSLSAQNLVDCCys63157
TGKLVSLSAQNLVDCCys62157
AFRGQYCCysYELDEKAVRPG2Vitronectin14
FRGQYCCysYELDEKAVRPG314
GQYCCysYELDEKAVRPG24
VPVPVFCCysDMTTEGGKWT2Microfibril-associated glycoprotein 43
VPVPVFCCysDMTTEGGKW23
NPGTFRILVGNKGCCysSHPS2von Willebrand factor12
NPGTFRILVGNKGCCysS312
  • a All 10 cysteinylated peptides derived from the four source proteins were identified in patient RA2, and the three peptides from cathepsin S were also found in patient LA2. The predicted P1 contact residues are shown in bold for HLA-DRB1*0401, underlined for DRB1*0101, and italicized for DRB1*1101. Because multiple binding registers were predicted for some 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. TEPITOPE does not model the binding of peptides with post-translational modifications; therefore, predictions of the P1 contact residues were based upon unmodified sequences.

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