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. 2023 Oct 19;42(7):1107–1117. doi: 10.1038/s41587-023-01945-y

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© Genentech, Inc. and Adaptive Biotechnologies Corp. 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a, Targeted immunopeptidomic workflow for the analysis of candidate neoepitopes within monoallelic cell lines expressing a polyantigen cassette. b, The number of targeted (blue) and detected (red) shared cancer neoantigen epitopes within each targeted assay. c, Comparison of TR-FRET RZ-score and NetMHC EL %Rank score for each epitope identified through targeted immunopeptidome analysis. d, NetMHC EL %Rank scores for neoepitopes detected in both untargeted and targeted (teal) analysis or targeted analysis alone (red). The box represents the interquartile range; the line represents the median value; and the whiskers represent the minimum and maximum values (excluding outliers). Each dot represents a neoepitope–HLA pair (untargeted & targeted n = 22, targeted only n = 64). The P value was calculated using a Wilcoxon test (two-sided). e, Same analysis as d but for TR-FRET RZ-scores. f, Summary of neoepitope–HLA pairs detected from shared cancer neoantigens. Color represents attomol of neoepitopes detected on column during analysis. Bolded squares with centered dots represent neoepitopes also detected in untargeted analysis. A square with an ‘X’ indicates A*02:01-specific neoepitopes that were detected in a cell line containing a polyantigen construct lacking control neoantigen sequences. a was created with BioRender.com.