Extended Data Fig. 4: Characterization of iPSC-derived cells by proteomic analysis.
a-d. Summary of LC-MS/MS and LFQ results (top), volcano plot of log2 LFQ ratio and -log10 p-values of all quantified proteins (middle), and enrichment analysis of biological processes of significantly dysregulated proteins in differentiated cells compared to iPSCs (bottom) for iEC (a), iPC (b), iSMC (c) and iAS (d). Red and blue circles indicate proteins that were significantly up- and downregulated respectively (n = 5 replicates/group, two-tailed t-test, p < 0,05). Dotted lines mark FDR threshold (p < 0,05). Proteins involved in colored enriched processes are marked with their gene name. Terms: Count: total enriched proteins, FE: fold enrichment, FDR: significance test of enriched terms. e. Correlation of expression levels of common (gray) and lineage-specific (colored) proteins between iEC vs pEC, iPC vs pPC, iSMC vs pSMC and iAS vs pAS. Black or colored line marks simple linear regression. f. Abundance of all lineage-specific proteins in iEC and pEC, iPC and pPC, iSMC and pSMC, iAS and pAS (n = 5 replicates/group). Bar graphs show mean ± SD.
