Extended Data Fig. 5: DVP applied to archival tissue of primary melanoma.

a, Isolation of tumor adjacent SOX10 positive melanocytes from a cutaneous melanoma tissue. Left: Contour alignment before laser microdissection. Right: Inspection after laser microdissection. b, Number of protein quantifications per sample type with n = 4 (melanocytes), n = 5 (stroma), n = 5 (melanoma in situ) and n = 13 (melanoma) independent replicates. Bar graphs represent mean of data and error bars are s.d. Samples were acquired in data-independent mode and analyzed with the DIA-NN software. c, Upper panel: Heatmap from Fig. 5h shown with identified protein clusters (color bar). Unsupervised hierarchical clustering based on all 1,910 ANOVA significant (FDR < 0.05) protein groups. Protein levels were z-scored. Lower panel: Pathway enrichment analysis of different row clusters obtained by unsupervised hierarchical clustering. The ReactomePA package was used for enrichment analysis with an FDR cut-off of 0.05 for all enriched terms. d, Relative levels (z-score) of proteins related to the KEGG term ‘melanogenesis’. Note, melanocytes show highest protein levels. The box plots define the range of the data (whiskers), 25th and 75th percentiles (box), and medians (solid line). Outliers are plotted as individual dots outside the whiskers. e, Pathway enrichment analysis of proteins up or down-regulated in vertical versus radial growth melanoma cells. Enrichment results were obtained with the ClusterProfiler R package³⁶ based on an FDR < 0.05.