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. 2020 Jan 27;11:532. doi: 10.1038/s41467-020-14381-2

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© The Author(s) 2020

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. 3 — a Overview of proteogenomics samples obtained from pre- and on-treatment core biopsies from the DP1 clinical trial. Each block indicates the data obtained from a separate core. b Microscaled proteogenomics achieves a high level of proteogenomics depth for the DP1 core needle biopsies. Table summarizing total proteogenomics coverage and numbers of mutated genes for all samples and average coverage across all analyzed cores is shown on the right. c The Venn-diagram shows the overlap between all genes identified across RNA-seq, proteomics and phosphoproteomics. d Heatmap summarizing proteogenomics features of the ERBB2 amplicon and adjacent genes at the level of CNA, RNA and protein expression. The set of genes in red make up the core of the ERBB2 amplicon and showed consistently high copy number amplification, RNA, and protein levels in all of the pCR cases (True ERBB2+ pCR set on the right) and in BCN1371 and 1369 (True ERBB2 + non-pCR set) but significantly lower protein levels in BCN1326 (False ERBB2+) and BCN1331 and BCN1335 (Psuedo ERBB2 + set). The arrow points to the amplified TOP2A gene in BCN1335. e The heatmap at the bottom shows corresponding Z-scores of RNA, protein, and phosphoprotein expression of ERBB1-4 across all 14 patients. ERBB3 protein and phosphoprotein and ERBB4 protein levels were also significantly lower in BCN1326, BCN1331 and BCN1335 than in the set of pCR cases.