Extended Data Figure 2. Correlation of protein abundance with MHC-I and MHC-II presentation.
Two mantle cell lymphoma cell lines, JEKO (left) and L128 (right) were digested with trypsin and peptides identified by LC-MS/MS. (a) Violin plots: distribution of protein abundance is plotted as kernel density violin plots with mean value indicated by a bar for all proteins (grey), proteins presented by MHC-I (blue), proteins presented by MHC-II (red), and mutated proteins where a mutated peptide was identified from whole proteome analysis (green). The distribution of protein abundance for each set of proteins (MHC-I presented, MHC-II presented, and mutated proteins) were compared to the distribution for all proteins by Kolmogorov-Smirnov test. For each line: *p<10−3; **p<10−5; ***p<10−9. (b) The abundance of each protein was estimated using the Histone ruler approach (black). Each protein with at least one peptide presented by MHC-I (blue) or MHC-II (red) is marked with an adjacent tick to the right and left (respectively) of the estimated protein abundance line. Proteins for which a mutated peptide was recovered by whole proteomic analysis (not from MHC immunoprecipitation) are indicated by ticks on the left of the figure (green). Noteworthy genes involved in MCL pathogenesis are highlighted. Proteins for which a mutated peptide was recovered by proteomic analysis are indicated by ticks on the left of the figure.