Figure 4

Quantitative proteome comparison of untreated, TGFβ-1, and TGFβ 1 + E64d treated iPL32 cells. (A) Workflow: I: Metabolic stable isotopic labeling (SILAC) of untreated cells with light “L”, TGFβ-1 treated cells with medium “M”, and TGFβ-1 + E64d treated cells with heavy “H” amino acids. II: Cell lysis and protein preparation. III: Quantification and combination of samples. IV: Fractionation, protein cleavage by trypsin, and peptide preparation for LC MS/MS analysis. (B) Venn diagram showing the total number of proteins identified in each independent experiment and in both experiments. (C) Density plot showing the distribution of Fc values (log₂) for the comparisons of the conditions untreated to TGFβ-1 as well as TGFβ-1 to TGFβ-1 + E64d in experiment 1. (D) Number of proteins altered in abundance in both experiments in the proteome comparison of untreated to TGFβ-1 treated cells as well as TGFβ-1 treated to TGFβ-1 + E64d treated cells. log₂ Fc ≤ 0.58 = less abundant; log₂ Fc ≥ 0.58 = more abundant. (E) KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis of proteins altered in abundance (log₂ Fc ≤ or ≥ 0.58) in the quantitative proteome comparison of untreated to TGFβ-1 treated iPL32 cells. Functional pathways significantly enriched (with p ≤ 0.05; ≥ 6 proteins in pathway) in the KEGG analysis are shown.