A targeted proteomics assay for the preoperative diagnosis of thyroid nodules.

Accurate preoperative diagnosis of thyroid nodules via fine-needle aspiration (FNA) biopsy remains challenging, particularly in cases with indeterminate cytology. This prospective, noninterventional, blinded, multicenter study establishes ThyroProt, a diagnostic classifier that integrates targeted mass-spectrometry-based quantification of a 3-protein signature with BRAF V600E mutation status, age, and gender. Developed and validated on 837 FNA samples, the classifier is evaluated in a prospective test set of 322 samples, achieving an area under the curve (AUC) of 0.94 with an overall accuracy of 90.7%. For the critical subgroup of Bethesda III/IV nodules, ThyroProt demonstrates an accuracy of 88.0%, with 82.4% sensitivity and 100% specificity. The classifier's robust performance is further evaluated in two independent multicenter cohorts, where it maintains an AUC of 0.87-0.91 and an accuracy of 84.3%-85.7%. This study supports the clinical utility of mass-spectrometry-based targeted proteomics for improving preoperative diagnosis of thyroid nodules, particularly those with indeterminate cytology.