Fig. 3

Representative spectra of quantified up-regulated and down-regulated ubiquitylated peptides. a Up-regulated ubiquitylated peptide from ubiquitin-like protein ISG15 precursor (aa30-44) with ubiquitylation of K35. The main figure shows the MS/MS spectrum and the corresponding ion coverage of the peptide to which the spectrum was assigned. The inset shows an enlarged region of the MS/MS spectrum (113.0 – 118.0 m/z) with the iTRAQ reporter ions. Based on the intensity of the 114.11 and 115.11 m/z (basal xenografts) and the 116.11 and 117.11 m/z (luminal xenograft) reporter ions, the peptide was determined to be up-regulated 2.69-fold in the luminal compared to the basal tumor sample. b Down-regulated ubiquitylated peptide from ATP-binding cassette sub-family E member 1 (aa235-252) with ubiquitylation of K250. The main figure shows the MS/MS spectrum and the corresponding ion coverage of the peptide to which the spectrum was assigned. The inset shows an enlarged region of the MS/MS spectrum (113.5 – 118.0 m/z) with the iTRAQ reporter ions. The peptide was determined to be down-regulated 2.36-fold in the luminal compared to the basal tumor samples