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. 2022 Mar 9;603(7902):721–727. doi: 10.1038/s41586-022-04499-2

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© The Author(s) 2022, corrected publication 2022

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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Extended Data Fig. 2 — (a) A heatmap depicting log2 peptide intensities for W>F substitution events in the proteome, selected to be reproducible across two biological replicates (1 column represents 1 replicate) in control (Ctrl) or IFNγ-treated (IFN) MD55A3-V5-ATF4^(1-63)-tGFP⁺¹ cells. Marked with an arrow is the peptide spanning the tryptophan at position 93 (W93) from the V5-ATF4^(1-63)-tGFP⁺¹ reporter. W>F substitutants are marked with a lower case “f”. (b-e) Heatmaps depicting substitutant peptide intensities detected specifically in mock (Ctrl) and IFNγ-treated (IFN) conditions; W>Y (b), W>C (c), W>Q (d) and W>H (e). (f) Scatter plot depicting protein expression calculated as log2 protein intensity from MS analysis in mock-treated (x-axis) and IFNγ-treated (y-axis) MD55A3-V5-ATF4^(1-63)-tGFP⁺¹ cells for all (grey) or substitutant (red) peptides. (g) Same analysis as in panel a, but for tryptophan (-W) and tyrosine (-Y) depletion. (h-j) Same analysis as presented in panels b-e, but for mock (Ctrl), tryptophan depletion (-W), and tyrosine depletion (-Y) conditions, for W>H (h), W>C (i) or W>A (j) comparisons. (k-l) Heatmaps depicting log 2 peptide intensities for W>F substitution events in the proteomes of glioblastoma cell lines HR0G2(k) and RA (l). (m) Heatmap depicting the number of substitutions peptides, as indicated, specifically detected in the proteomes of IFNγ−treated or control glioblastoma HROG02 cells. (n) A Venn diagram (same as Fig. 2f) depicting the overlap between the substitutant peptides specifically detected in IFNγ-treated or tryptophan-depleted MD55A3-V5-ATF4^(1-63)-tGFP⁺¹ cells with the names of the overlapping proteins indicated.