Fig. 4.

Isotopic labeling of HLA-A*68:01 ligands in the presence of proteasome inhibitors. A total of 42 ion peaks were analyzed with both 20 μm MG-132 and 2.5 μm epoxomicin. Their elution position in HPLC (Fraction N), monoisotopic mass (M+H⁺), the number of Arg (R) or Lys (K) residues, which was inferred from the isotopic peak that increased upon ¹⁵N-labeling, and the labeling ratio (Ratio: see Exp erimental Procedures), are indicated. Peptides were classified as inhibitor-sensitive or -resistant when the labeling ratio was <0.35 or >0.6, respectively, with both inhibitors. Underlined labeling ratios for some inhibitor-sensitive ligands indicate distorted values due to inhibition of labeling close to background levels. When the labeling ratio showed intermediate values or was significantly different with both inhibitors, the peptides were not assigned. Within each set, the peptides are ordered by their M+H⁺. Ion peaks that were sequenced are indicated (see Tables 3S and 4S for full labeling data).