In our study, we constructed a multicenter thyroid-cancer cohort consisting of 467 formalin-fixed paraffin-embedded (FFPE) samples, among which WES, proteome, and phosphorylated proteome analysis were conducted. Thyroid tumors consisted of 124 ATC samples, 47 PDTC samples and 177 PTC samples (including 3 biological replications).The 119 NATs were derived from tumor-adjacent tissues of 20 ATC patients and 99 PTC patients. Phosphoproteomic analysis was performed on 63 ATCs, 25 PDTCs, and 81 PTCs. 48 NAT samples were determined from tumor-adjacent tissues of 20 ATC patients and 28 PTC patients.