Comparison of primary cell differentiation with that of MEL, G1ER, and MEDEP cells. (A) Evolution of the total protein content throughout the differentiation process. The total protein content was calculated by summing the amounts of each protein quantified by MS analysis. (B) Comparison of the primary cell (PC) proteome throughout the differentiation process with the proteomes of MEDEP, MEL, and G1ER cells. Values correspond to Pearson correlation coefficients. (C) Hierarchical clustering analysis of protein expression during TED of MEL, G1ER, MEDEP, and PCs. Protein expression values were z-score transformed before clustering analysis. (D) Comparison of the expression pattern and the absolute protein expression in PCs and cells from cellular models. Each point corresponds to one of the proteins quantified in both PCs and the cell line. The Pearson correlation coefficient of the expression pattern (x-axis) was calculated after z-score transformation of the quantification values. The ratio of the median expression value in the cell line to the median expression value in PCs is indicated (y-axis). Right: Gene Ontology cellular component term enrichment analysis. Annotations (triangles) are superimposed on individual protein data. The coordinates of the crosses correspond to the median values of all proteins carrying the concerned annotation. (E) PCA of the proteome evolution in the different cellular models. Log₂ of the expression values were used for this analysis: green dots, MEL cells; blue dots, G1ER cells; orange dots, MEDEP cells; red dots, PCs.