Fig. 1

Integrated proteomic profiling of Ubash3b knockdown in p210 BCR-ABL cells. a The experimental workflow for integrated phosphotyrosine, total proteome, and interactome analysis. BaF3 cells harboring BirA*-p210-BCR-ABL upon Ubash3b KD (SILAC labeled: Light) and Luciferase KD (SILAC labeled: Heavy) were mixed in equal protein amounts and trypsin digested followed by immunoprecipitation by pan-phosphotyrosine antibody (phosphotyrosine analysis) and basic HPLC fractionation (total protein analysis) analyzed by LC-MS/MS. For BioSITe, SILAC labeled cells were treated with biotin and mixed in equal protein amount for trypsin digestion and anti-biotin antibody immunoprecipitation (p210 interactome) followed by LC-MS/MS analysis. b Waterfall plot for log₂ fold-changes of tyrosine phosphorylated peptides in Ubash3b KD cells over control. c Relative abundance of biotinylated proteins by p210 BCR-ABL (log₂ intensity ratio of Ubash3b KD/control cells). d Tyrosine hyperphosphorylated sites of proteins in Ubash3b KD compared to control and grouped into their molecular class. e p210 proximal proteins upon Ubash3b KD that increase, remain unchanged and decrease