Additional file 2 of Phospho-heavy-labeled-spiketide FAIMS stepped-CV DDA (pHASED) provides real-time phosphoproteomics data to aid in cancer drug selection

Additional file 3: Table S1. SBDS heavy-labeled phosphorylated peptide standards. Table S2. Common and unique phosphoproteins identified across all four CVs based on PSM acquisition. Table S3. High confidence modification sites identified in LFQ (p < 0.01). Table S4. High confidence modification sites identified in pHASED (p < 0.01). Table S5. Unique and common phosphoproteins identified in LFQ and pHASED datasets. Table S6. Phosphorylated master protein kinases identified in LFQ dataset (p < 0.01). Table S7. Phosphorylated master protein kinases identified in pHASED dataset (p < 0.01). Table S8. FLT3-D835 mutations associated with resistance to tyrosine kinase FLT3 inhibitors. Table S9. Kinase-Substrate analysis of LFQ dataset for resistant cells in comparison to FLT3-ITD (log2 fold change ± 0.5). Table S10. Kinase-Substrate analysis of pHASED dataset for resistant cells in comparison to FLT3-ITD (log2 fold change ± 0.5). Table S11. Canonical pathways identified as significantly associated with LFQ dataset for resistant cells in comparison to FLT3-ITD. Table S12. Canonical pathways identified as significantly associated with pHASED dataset for resistant cells in comparison to FLT3-ITD. Table S13. Kinase activity inferred by KSEA analysis of phosphorylation changes in pHASED dataset (log2 ± 0.5, p ≤ 0.05) for resistant cells in comparison to FLT3-ITD. Table S14. Mutation-specific response to sorafenib. IC50 compared to FLT3-ITD. Table S15. Bliss Synergy scores for sorafenib in combination with KU-60019 at different doses. Table S16. Unique ATM substrates identified with increased phosphorylation (log2 ≥ 0.5) in pHASED dataset for resistant cells in comparison to FLT3-ITD. Table S17. Vector mutations in FLT3 gene.

附加文件3：表S1。SBDS重同位素标记磷酸化肽段标准品。
表S2：基于肽谱匹配（PSM, Peptide Spectrum Matches）的获取结果，在全部4个CV样本中鉴定得到的共有及特有磷酸化蛋白质。
表S3：在Label-free定量（LFQ, Label-free Quantification）数据集内鉴定得到的高置信度修饰位点（p < 0.01）。
表S4：在pHASED数据集内鉴定得到的高置信度修饰位点（p < 0.01）。
表S5：在LFQ及pHASED数据集中鉴定得到的特有及共有磷酸化蛋白质。
表S6：在LFQ数据集中鉴定得到的磷酸化核心蛋白激酶（p < 0.01）。
表S7：在pHASED数据集中鉴定得到的磷酸化核心蛋白激酶（p < 0.01）。
表S8：与酪氨酸激酶FLT3抑制剂耐药相关的FLT3-D835突变。
表S9：相较于FLT3-ITD突变型细胞，耐药细胞LFQ数据集的激酶-底物分析结果（log2倍变化±0.5）。
表S10：相较于FLT3-ITD突变型细胞，耐药细胞pHASED数据集的激酶-底物分析结果（log2倍变化±0.5）。
表S11：相较于FLT3-ITD突变型细胞，与耐药细胞LFQ数据集显著相关的经典通路。
表S12：相较于FLT3-ITD突变型细胞，与耐药细胞pHASED数据集显著相关的经典通路。
表S13：基于激酶-底物富集分析（KSEA, Kinase-Substrate Enrichment Analysis），对相较于FLT3-ITD突变型细胞的耐药细胞pHASED数据集内的磷酸化变化（log2±0.5，p ≤ 0.05）推断得到的激酶活性。
表S14：针对索拉非尼的突变特异性应答及其半数抑制浓度（IC50, Half Maximal Inhibitory Concentration）与FLT3-ITD的对比结果。
表S15：不同剂量下索拉非尼与KU-60019联合使用的Bliss协同得分。
表S16：相较于FLT3-ITD突变型细胞，耐药细胞pHASED数据集中磷酸化水平上调（log2 ≥ 0.5）的特有毛细血管扩张性共济失调突变（ATM, Ataxia Telangiectasia Mutated）激酶底物。
表S17：FLT3基因的载体突变。