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. 2024 May 29;11:551. doi: 10.1038/s41597-024-03394-x

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — iPTMs detection of perturbation-induced and endogenous peptidoforms. (A) Pre-normalisation PSM counts for prey (density plots) and bait (dots) proteins for AMG-510 treated (blue) and untreated (salmon) samples for KRAS^WT and KRAS^G12C mutant cell lines, for each replicate IP-MS experiment. (B) Differential bait peptidoforms detected between AMG-510 and untreated KRAS^G12C samples according to the SAINTexpress, defined as BFDR <0.05. Only bait peptidoforms were included in the SAINTexpress analysis. (C) Structural model of C118 position relative to AMG-510 and GDP binding site in KRAS^G12C protein. (D) Pre-normalisation PSM counts for prey (density plots) and bait (dots) proteins for IgG control (top) and endogenously enriched BRD4 across cell lines, for each replicate IP-MS experiment. (E) Clustering of post-normalised PSM counts for highly abundant peptidoforms belonging to bait BRD4 protein, excluding the IgG control samples. Unsupervised clustering performed with default hclust parameters with peptidoforms not detected in specific samples assigned a zero value following log transformation. (F) Differential bait BRD4 peptidoforms detected between K-562 and MOM-13 samples according to the SAINTexpress, defined as BFDR <0.05. Only bait peptidoforms were included in the SAINTexpress analysis.