Detection and characterization of peptide NS3_1406–1415 in MHC class I ligands isolated from UNS3-4A/A2-27.35 cells.

<p>Naturally processed MHC class I ligands of UNS3-4A/A2-27.35 cells were separated by high performance liquid chromatography (HPLC) and analyzed by mass spectrometry. (A) A chromatogram of the total ion current (TIC) is shown. (B) The mass chromatogram of ionized peptides with m/z = 499.3 reveals a peak at retention time t = 49.5 min that correlates with (C) a signal of the synthetic peptide NS3_1406–1415 (KLVALGINAV) which elutes after 51.3 min. In all graphs, HPLC retention times are shown on the abscissa and relative signal intensity on the ordinate. Small insets in panels B and C show mass spectra of peptides eluted at the indicated time points. (D) MSMS spectrum of the synthetic peptide NS3_1406–1415 (KLVALGINAV). (E) MSMS spectrum of the natural peptide isolated from UNS3-4A/A2-27.35 cells, revealing amino acid sequence KLVALGINAV identical to the synthetic peptide shown in panel A. Identified amino acid sequences of peptide fragments are indicated on the top of the peaks. Due to the protonated N-terminal lysine residue, the b series of peptide fragments is dominating the MSMS spectra.