Relative Quantification of Differentially Expressed MHC I peptides and Source mRNAs from Thymocytes and EL4 Cells
 (A) Volcano Plot representation illustrate MHC I peptides reproducibly detected across biological replicates (n = 3). Peptides over- and underexpressed on EL4 cells relative to thymocytes (p-values≤0.05; fold change ≥ 2.5) were highlighted in blue and red, respectively. MS-MS spectra of circled peptides are shown in B and C.
 B) Scatter plot shows the correlation between relative expression of mRNA and that of MHC I peptide. Expression ratios for source mRNA (x axis) and MHC I peptide (y axis) between EL4 cells and thymocytes were plotted on a log 2 scale for 47 pairs. A Spearman correlation coefficient was calculated from the linear regression. MHC I peptides overexpressed in EL4 cells or normal thymocytes are highlighted in blue and red, respectively; peptides that were not differentially expressed are in grey. Dashed box includes peptides whose overexpression on EL4 cells did not correlated with increased mRNA levels of their source protein.