Reagents
Cell culture and SILAC labeling
Cell viability assay
Cell stimulation, lysis, and Western blotting
Immunoprecipitation
RNAi and transfection
Caspase-3/7 activity measurements
Sample preparation for MS-based interactome analysis
Sample preparation for MS-based phosphotyrosine interactome analysis
Sample preparation for MS-based phosphoproteome analysis
TMT labeling and phosphopeptide enrichment
Sample preparation for MS-based proteome analysis
Liquid chromatography–tandem mass spectrometry
MS data analysis
Bioinformatic analysis
Statistical analysis of MS data is described in the previous section. For experiments with effects measured as fold changes relative to a control within each experiment, fold changes were log2 transformed and statistical significance was determined on the basis of a one-sample t test asking if the mean (of minimum three independent experiments) was different from 0 (Fig. 5, B to E, and fig. S7B). Significance testing for data in fig. S5 (D and E) was performed by a two-sample t test with a Sidak-Bonferroni correction for multiple testing. A statistically significant difference was concluded when P < 0.05.