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Significance Phosphotyrosine (pTyr)-dependent protein complexes are key machinery for regulating cancer signaling. We developed the Photo-pTyr-scaffold approach for unbiasedly capturing and exploring weak and dynamic pTyr protein complexes. By utilizing the Src kinase Src homology 2 superbinder with nanomolar binding affinity, Photo-pTyr-scaffold showed superior sensitivity for profiling native pTyr protein complexes in cancer cells and breast tumor samples. Importantly, we discovered PDGFRB to be a critical signaling node for mediating intercellular cancer signaling, which is highly expressed but independent of ERBB2, the well-established breast cancer therapeutic target. Our results could lead to new targeted therapies for breast cancer and generic approaches for exploring dynamic protein complexes related to other types of protein posttranslational modifications and discovering biomarkers readily from complex clinical samples.

Photoaffinity-engineered protein scaffold for systematically exploring native phosphotyrosine signaling complexes in tumor samples