Extended Data Fig. 6. Validation of five substitutants epitopes identified in RA cells.

The identification of five substitutant peptides was validated with targeted mass spectrometry. The co-elution profiles of the transitions of spiked-in synthetic heavy-labelled peptides and endogenous eluted HLA bound peptides are shown in two biological replicates of RA cells treated with IFNγ (each in two technical replicates R1 and R2). The quality control (QC) analysis of the pool of synthetic peptides is provide for comparison. The MS/MS fragmentation pattern further confirms the presence of the endogenous peptide (Δm = 10 Da for F and Δm = 7 Da for L). Labelled amino acids are shown in bold.