Figure 1.

Proteomic analysis of patient-derived lung tumour ECM. (A) Summary of the workflow for the collection of tissue samples, isolation of insoluble (insol.) ECM proteins and MS-based proteomic analysis of the lung tumour matrisome. Frn, fraction. (B) Over-representation analysis of GO cellular component terms in the dataset of proteins quantified by MS-based proteomics. The top ten most enriched terms are shown (P < 0.01, Fisher’s exact test with Benjamini–Hochberg correction). All enriched terms are provided in Supplementary Data 2 . (C) Distribution of proportions of protein sequences (proportions of possible tryptic peptides per protein) covered by unique peptides identified by MS. (D) Distribution of log₁₀-transformed spectral counts per protein. Statistical analysis for c and d, two-sided Welch’s t-test (n = 1,420 and 2,182 proteins for extracellular proteins (those annotated with GO term extracellular region) and other proteins, respectively). Black circle, median; white bar, 95% confidence interval; silhouette, probability density. (E) Volcano plot of lung tissue proteins quantified by MS-based proteomics. Significantly differentially regulated proteins enriched or depleted by at least two-fold are coloured orange; differentially regulated matrisome proteins are indicated with large coloured circles (red, increased in tumour; blue, decreased in tumour) (P < 0.05, paired two-sided Student’s t-test with Benjamini–Hochberg correction). Selected proteins are labelled with gene names for clarity. (F) Principal component analysis of lung tissue samples analysed by MS-based proteomics.