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. 2023 Feb 6;14:643. doi: 10.1038/s41467-023-36314-5

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© The Author(s) 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. 6 — a Experimental workflow showing analysis of protein extracts by mass spectrometry. b Unique and overlapping protein identifications subdivided by treatment condition in lungs and BALF by biological fluid. c Response profile heatmaps displaying protein expression across treatment conditions in each biological fluid. d Volcano plot depicting differentially expressed proteins in BALF (top panel) and lung (bottom panel) with proteins associated with significant gene ontology (GO) terms highlighted in each plot. e, f Specific lung proteins downregulated following Bleo/TH5487 treatment compared to the Bleo alone condition. Proteins highlighted in these plots are specifically associated with e fibrotic-related changes or f SMAD (top panel) and nucleotide base repair (bottom panel). g Network analysis (StringDB) comparing the Bleo/Bleo+TH treatment condition displaying significant biological GO terms, protein counts in the network, strength, and FDR. For LCMS/MS analyses, murine samples were analyzed by single-shot DIA-MS for cohorts Bleo (B) n = 5, bleomycin/TH5487 (BTH) n = 5, bleomycin/dexamethasone (DEX) n = 4, TH5487 only (TH) n = 4 and vehicle only (V) n = 4, respectively. Significance criteria; absolute fold-change ≥2 & FDR, Benjamini–Hochberg-corrected p-value ≤0.05 unless indicated otherwise. Source data are provided as a Source data file. Elements of this figure were created with BioRender.com.