Fig. 4.

Label-free semi-quantitative comparative analysis of IFNγ modulated immunopeptidome. A, Reproducibility calculated by Pearson correlations of log2 transformed intensities from HLA-Ip of control and IFNγ -treated samples across the different MS measurements. B, Number of HLA-Ip identified from UWB.1 289 ovarian cancer cells untreated (control) and treated with IFNγ. The number of peptides identified with (gray) and without (blue) matching identifications across the treated and untreated samples and the average values of the Pearson correlations are indicated. C, Summed peptide intensities identified in each of the IFNγ treated and control samples. D, Volcano plot summarizing unpaired t test analysis of the immunopeptidome of IFNγ treated versus untreated cells. Peptides located above the lines are statistically significantly modulated in their level of presentation (FDR = 0.01, S0 = 1). All peptides derived from proteins related to immunity are highlighted in pink. Selected up-regulated peptides were highlighted in red, corresponding to well known intracellular mediators of IFNγ signaling. E, Volcano plot of unpaired t test analysis of the proteome of IFNγ treated versus untreated cells. Proteins located above the lines are statistically significantly modulated in their expression level (FDR = 0.01, S0 = 0.2). Selected proteins involved were similarly highlighted.