Extended Data Fig. 1: Proteogenomic analysis of PDAC.
a, The workflow for proteogenomic analysis of PDAC. Exome-sequencing analysis of cancer tissues and blood samples and RNA-sequencing of cancer tissues were performed for tissue samples from 196 patients while mass spectrometry-based proteomic analyses (global proteome and phosphoproteome) were performed for high purity samples (cellularity ≥ 19%) from 150 patients. Distribution of tumor cellularity was shown for 196 samples (bottom left). Only the samples with cellularity ≥ 15% were used for the analysis. In the box plot, the center line indicates median value and the box limits indicate upper and lower quartiles. b, Numbers of non-redundant peptides identified from global proteome and phosphoproteome data. c, Numbers of protein-coding genes identified from mRNA sequencing and proteome data (global proteome and phosphoproteome). The average numbers of peptides and protein-coding genes are indicated in (b) and (c), respectively. d, Numbers of somatic mutations altering protein sequences and genes carrying the mutations identified from exome-sequencing data. e, Relationships among significantly mutated genes (SMGs) identified from our cohort and previous cohorts of the TCGA10, Bailey et al.11, Biankin et al.12, Waddell et al.13, and Witkiewicz et al.14.
