Additional file 2 of Isotypes of autoantibodies against novel differential 4-hydroxy-2-nonenal-modified peptide adducts in serum is associated with rheumatoid arthritis in Taiwanese women

Additional file 2: Fig. S1. Differential 4-hydroxy-2-nonenal (HNE)-modified peptide adducts were re-analyzed through PEAKS 7 using previous MS/MS spectra (ProteomeXchange: PXD004546). Acquired MS/MS spectra were obtained through pooled concanavalin (Con) A-captured serum proteins (nine rheumatoid arthritis (RA) and nine healthy control (HC) pooled samples), 1-D SDS-PAGE, in-gel digestion, and nano-LC-MS/MS (A). HNE reacts with amino acid residues of proteins to form HNE-protein adducts by Michael addition and Schiff base adducts, respectively (B). Representative MS/MS spectrum of the 1211-SHTLRTTCWDGKLEYPTCAK-1230 peptide sequence and the modified peptide bearing an HNE modification at the K1230 residue in RA patients (C). A representative MS/MS spectrum of the peptide sequence 78-AVGDKLPECEADDGCPKPPEIAHGYVEH SVR-108 and the modified peptide bearing the HNE modification at the C92 residue in RA patients (D). The MS/MS spectrum 2-TVAAPSVFIFPPSDEQLK-19 and the modified peptide bearing the HNE modification at the A5 residue in RA patients (E, upper panel); 2-TVAAPSVFIFPPSDEQLK-19 and the modified peptide bearing the HNE modification at the A4 residues in RA patients and HCs (E, bottom panel). Representative MS/MS spectrum of 328-TFGSGEADCGLRPLFEKK-345 and the modified peptide bearing the HNE modification at the K344 residue in RA (F). The MS/MS spectrum 284-HRTGDEITYQCRNGFYPATRGNTAK-308 and the modified peptide bearing the HNE modification at the K308 residue in HCs (G). A representative MS/MS spectrum of the peptide sequence 162-ILGGHLDAK-170 and the modified peptide bearing the HNE modification at the A169 residues in HCs (H). Representative MS/MS spectrum of 83-VYACEVTHQGLSSPVTKSFNR-103 and the modified peptide bearing the HNE modification at the Q91 residue in HCs (I). The MS/MS spectrum 328-TFGSGEADCGLRPLFEK-344 and the modified peptide bearing the HNE modification at the C336 and L341 residues in HCs (J).