Extended Data Fig. 5: Extended analysis of pTyr protein complex and pTyr site profiling and integrated analysis of ligand–receptor–downstream signalling axes.

a, Clinical tissue samples used for N-glycoproteomic analysis, photo-pTyr-scaffold, and pTyr peptide enrichment. b, Overlap of pTyr writers, readers, and erasers identified by photo-pTyr-scaffold approach and pTyr peptide enrichment approach. c, Summary of all the pTyr writers, readers, and erasers identified by two approaches in Fig. 4b. The rectangle indicates proteins identified by the photo-pTyr-scaffold approach and the circle indicates the pTyr sites identified by pTyr peptide enrichment approach. Proteins are classified according to their molecular functions. d, Expression levels and pTyr sites of top ranked pTyr writers, erasers and readers in Fig. 4c. Box plots are as defined in Fig. 2c. P values are from two-tailed unpaired Student’s t-test. e, The overlapped GOBP terms of proteins identified by our multidimensional proteomics (S–PM and pTyr machinery proteins identified in tumour tissues by N-glycoproteomic profiling and pTyr-mediated complexes profiling) with the core signalling pathways summarized from global genomic analysis of PDAC^77,78. The core signalling pathways summarized in these two references were combined. P values are from hypergeometric distribution. f, The four categories of activated ligand–receptor–downstream signalling axes in which the expression of both receptor and downstream protein were significantly changed in tumours in the pTyr signalling dataset (circles labelled with P). g, Spatial and temporal annotation of the 148 pairs in Fig. 4d. h, The activated paracrine signalling pairs from stromal cells to PCCs in tumour and their downstream proteins screened out from g.