Bioinformatics analysis incorporating the K562 core proteome significantly reduces the pulldown dataset volume for each drug, the interactomes of which display substantial differences. (A) Schematic representation of the workflow of chemical proteomics experiments and core proteome analysis, annotated for different stages with the respective number of proteins (italics). (B) SDS-PAGE result of a 4% to 12% gradient gel after silver staining of a K562 pulldown set prior to band excision and further processing for MS analysis. All 3 displayed lanes are derived from the same gel. Significant bands, corresponding to the TEC family kinases (BTK, TEC), SRC family kinases, c-SRC kinase CSK, and the oxidoreductase NQO2, as well as regions corresponding to BCR-ABL, DDR1, and ABL are labeled.