Potential Markers for Thyroid Neoplasms in the Upstream Analysis of the Plasma Proteome

The reliability of existing diagnostic methods for thyroid neoplasms remains questionable, which necessitates the search for alternative approaches. The use of nontarget proteomic analysis for diagnosing oncological diseases is gaining traction and represents an efficient method for multiplex analysis. This study analyzed 372 blood plasma samples collected from patients with histologically confirmed thyroid pathologies treated at the National Medical Research Center for Endocrinology in 2019-2021. The samples were obtained prior to surgical intervention. Sample preparation involved the reduction and alkylation of disulfide bonds, followed by proteolysis and purification using specialized cartridges. Proteomic analysis was performed using nanoflow HPLC coupled with high-resolution mass spectrometry in a data-dependent acquisition mode. Peptides were identified using FragPipe software, and their suitability for biomarker discovery was assessed. From this analysis, 60 candidate proteins for thyroid disease biomarkers were identified, and sequences of 2930 peptides were evaluated. Further evaluation of nine candidate proteins revealed 31 peptides with high suitability scores for quantification. These peptides can be consolidated into a single biomarker panel that will be further developed for the risk stratification of patients with thyroid diseases.