95 (Phospho)proteomics biomarkers for sunitinib response in RCC – 713) phosphosites per sample. Identified and quantified phosphosites and phosphopeptides are presented in Supplementary Tables 2 and 3. The primary analysis, aiming to identify markers distinguishing sensitive from resistant patients, was performed on phosphosite data. Unsupervised cluster analysis of all identified phosphosites could not separate sensitive from resistant patients (Supplementary Figure 1a). After data filtering (p < 0.05, FC > 2) (Figure 1a), a signature of 78 differential phosphosites was identified, comprising 22 upregulated sites in resistant patients; 4 of these were uniquely identified in resistant patients (BCAR3, NOP58, EIF4A2 and GDI1, filtered for ≥ 30% data presence in the group with highest abundance). Fifty-six phosphosites of aforementioned signature were upregulated in sensitive patients; 35 of these were uniquely identified in this subgroup (Table 2). This selection of most differential phosphosites split by group is shown in Figure 1b. Top-10 differential phosphosites in each group are shown in Figure 1c. Phosphopeptide clustering data are available in Supplementary Figure 2a and 2b. 4
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