Table I

Number of spectra, peptides, source proteins, and decoy hits identified from each patient's HLA-DR molecules in synovial tissue

PatientsAll samples combined
RA1RA2LA1LA2
HLA-DR genotype0402/11040101/04010101/08011001/1101
MS/MS spectra1,6471,7122,2371,6647,260
Spectrum-to-peptide matches497 (30%)715 (42%)685 (31%)361 (22%)2,258 (31%)
Peptides identified by ≥2 programs277 (17%)466 (27%)464 (21%)220 (13%)1,427 (20%)
Non-redundant sequencesa85 (5%)89 (5%)104 (5%)57 (3%)262 (4%)
Source proteinsb63707445166
Decoy hitsc03104
False discovery rate (%)0.6
  • a Number of peptides with no overlapping amino acid sequences.

  • b Number of proteins from which HLA-DR-bound peptides were identified.

  • c Number of spectrum-to-peptide matches to the decoy database.