Fig. 3: Definition of medulloblastoma-associated proteins and peptides based on class II immunopeptidome analyses.

Saturation analysis showed that 71% and 66% of the estimated maximum attainable amount of distinct HLA class II-presented proteins (a) and peptides (b) had been identified, respectively. c Comparative profiling of the HLA class II peptidome of medulloblastoma versus an in-house benign database revealed medulloblastoma-associated source proteins (n = 60), which were identified on at least two neoplasms (enlarged view on the left). Each bar in this waterfall plot (x-axis) represents a single source protein. In contrast, the y-axis depicts the frequency of positive immunopeptidomes for medulloblastoma (n = 28) and benign samples without testes (n = 364 covering 30 different human tissues). The Venn diagram on the right compares the overlap of HLA class II peptides between tumors and benign samples (d). A set of 10 tumor-associated proteins naturally presented on 11–36% of medulloblastomas was defined and is depicted in the bar plot. e Comparative profiling of HLA class II peptides on medulloblastoma identified n = 11,613 medulloblastoma-associated peptides, whose source proteins were subjected to hotspot analysis. The Venn diagram on the left illustrates the total number of HLA class II-restricted peptides. Waterfall plots (c,e) were generated in three steps, 1. descending sorting by detection frequency (multiplied with −1) on normal samples, whereby a single detection on non-CNS tissues is treated equally to 0 detections, 2. descending sorting by detection frequency on tumors, 3. descending sorting by ratio of absolute detection numbers on tumors/absolute detection numbers on tumors + normal samples. As in the step before, a single detection on non-CNS tissues is treated equally to 0 detections. Source data are provided as a Source Data file.