Fig 6. MS/MS spectra of cross-linked products in PPAR-β/δ.

(A) MS/MS spectrum of a 3+ charged cross-linked product at m/z 673.033, identified in experiments with the urea-linker. The cross-linked product was unambiguously identified based on the presence of a y₃ ion at m/z 374.251 (β-peptide) and a y₁₁ ion at m/z 1262.640 (α-peptide). The specific fragmentation pattern of the urea-linker is described as “Bu” and “BuUr”.[15] (B) MS/MS spectrum of a 3+ charged cross-linked product at m/z 820.104, identified in experiments with the zero-length cross-linker DMTMM. The cross-link between the N-terminus of the LBD (Gly-167) and Glu-373 was identified based on a b₁ ion at m/z 1196.661 (α-peptide) and a b₂ ion at m/z 1283.700 (β-sequence). { denotes the N-terminus of the protein.