Extended Data Fig. 7: Identification of MHC-I human ALK peptides in human ALK+ cell lines. | Nature Cancer

Extended Data Fig. 7: Identification of MHC-I human ALK peptides in human ALK+ cell lines.

From: ALK peptide vaccination restores the immunogenicity of ALK-rearranged non-small cell lung cancer

Extended Data Fig. 7

(a) Identification of ALK-specific peptides by discovery mass spectrometry from pan-HLA immunoprecipitations of the ALCL cell line Karpas-299. (b) Poisson LC-DIAMS plots from pan-HLA immunoprecipitations of the ALK+ ALCL cell lines Karpas-299. Poisson plots combine an extracted ion chromatogram (XIC) for the peptides’ precursor m/z (black trace) with an inverted, scaled Poisson chromatogram (blue trace, see Methods). Peptide detection (see Methods) at an elution point is associated with coincident precursor and Poisson peaks, here marked by blue arrows The elution position lies near the predicted elution position determined by a retention time peptide set added to the Karpas-299 (b, lower panel) samples and, after sample data was collected, the synthetic set of ALK peptides. (c) Poisson analysis of the same LC-DIAMS datasets detecting AMLDLLHVA in DEL but not in NCI-H2228, using reference information for a set of common HLA-A*02:01 peptides, identifies substantially better A02:01 peptide recovery from NCI-H2228. Hence, that NCI-H2228 cells do not present HLA-A*02:01 peptides from ALK, including the strong binding AMLDLLHVA peptide detected in the ALCL cell line DEL, cannot be associated with poor overall recovery of A*02:01 peptides.

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