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After high-speed centrifugation of 20,000×g at 4 °C, supernatants were quantified via Bradford assay. Equal protein amounts underwent DTT reduction and IAA alkylation, then digested overnight with trypsin. Digests were acidified and desalted. Subsequently, intact N-glycopeptides were enriched by HILIC beads, while phosphopeptides were isolated via Ti⁴⁺-IMAC affinity beads with sequential washing and elution steps. Desalted whole peptides, enriched N-glycopeptides and phosphopeptides were vacuum-dried for subsequent detection.  The LC-MS analysis was performed using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific) coupled with an Easy‑nLC 1200 nano‑liquid chromatography system. Peptide separation was performed on an analytical column (15 cm × 75 μm, IonOpticks). Global proteome samples were separated with a 60-min LC gradient, whereas phosphoproteome and N-glycoproteome samples were subjected to a 95-min LC gradient. For global proteome and phosphoproteome, data were acquired in data‑independent acquisition (DIA) mode. For N-glycoproteome, data were acquired in data‑dependent mode (DDA) mode."],"repository":["Pride"],"modification":[""],"quantification_method":["Not available"],"data_protocol":["For global proteome and phosphoproteome, raw DIA files were processed using Spectronaut (v19.9) against the Mus musculus UniProt reviewed database (downloaded March 2025). Up to two missed tryptic cleavages were allowed. Carbamidomethylation (C) was set as a fixed modification; oxidation (M) was set as a variable modification. False discovery rate (FDR) was controlled to 1% at peptide‑spectrum match, peptide, and protein levels. DirectDIA search was applied with peptide length restricted to 7-52 amino acids; other parameters were set as default. For phosphoproteome analysis, phosphorylation (S/T/Y) was added as an additional variable modification.   For the N-glycoproteome, raw files were analyzed using Glyco‑Decipher (v1.0.5) against the Mus musculus UniProt reviewed database (downloaded March 2025). Search parameters included: full tryptic specificity; precursor mass tolerance, 10 ppm; fragment mass tolerance, 20 ppm; up to three missed cleavages. Fixed modification: carbamidomethylation (C). Variable modification: oxidation (M). FDR for glycopeptide‑spectrum matches was controlled below 1%."],"omics_type":["Proteomics"],"labhead":["Qing Zhou"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Department of Ophthalmology, Children's Hospital of Nanjing Medical University, Nanjing, China"],"species":["Mus Musculus (mouse)"],"publication":["42769305 Xu K, Zhou Q. Integrated multi-omics atlas reveals PTM-driven signaling and immunologic remodeling in a mouse model of age-related subclinical hypothyroidism. Am J Transl Res. 2026 18(8):7075-7091 10.62347/pqye9899"],"submitter_mail":["edgarkun1976@sina.com"],"submitter_affiliation":["Jiangsu Province Hospital of Chinese Medicine，General Surgery"],"submitter_country":["China"],"pubmed_abstract":["<h4>Objective</h4>Age-related subclinical hypothyroidism (AR-SCH) profoundly impairs thyroid structural and functional integrity in the elderly, yet the systemic molecular architecture driving AR-SCH pathogenesis remains poorly understood. This study aimed to construct a comprehensive multi-omic atlas of the AR-SCH mouse thyroid.<h4>Methods</h4>Global proteomics, site-specific N-glycoproteomics, and phosphoproteomics were integrated to profile thyroid tissues from AR-SCH and control mice.<h4>Results</h4>In total, 6,666 proteins, 2,476 site-specific N-glycans, and 11,929 phosphorylation sites were identified. Global proteomics revealed a widespread reduction of functional proteins (81.7% downregulated), primarily associated with cytoskeletal structural remodeling and tissue degeneration under AR-SCH conditions. N-glycoproteomics identified altered fucosylation and reduced N-glycosylation associated with extracellular-matrix organization and local immune-related processes. Furthermore, an extensive hypophosphorylation trend (91.53% downregulated sites) was associated with suppression of intracellular signaling cascades, possibly involving autophagic clearance and perturbed apoptotic homeostasis.<h4>Conclusion</h4>Multi-omics integration suggests an interconnected network as a convergent hallmark of AR-SCH progression, characterized by cytoskeletal reconfiguration, immune regulation shifts, and signaling attenuation that synergistically contribute to systemic thyroid decline, offering a therapeutic window for preserving endocrine homeostasis."],"pubmed_title":["Integrated multi-omics atlas reveals PTM-driven signaling and immunologic remodeling in a mouse model of age-related subclinical hypothyroidism."],"pubmed_authors":["Xu Kun K, Zhou Qing Q"],"additional_accession":[]},"is_claimable":false,"name":"Multi-Omic Signatures of Thyroid Damage in Age-Related Subclinical Hypothyroidism","description":"Age-associated subclinical hypothyroidism (AR-SCH) causes severe structural and functional damage to thyroid glands in aged populations, but the global molecular mechanisms governing AR-SCH pathogenesis are largely unclear. We constructed an exhaustive multi-omic map of thyroid tissues from AR-SCH mice via integrated global proteome, site-specific N-glycoproteome and phosphoproteome analyses. Altogether, we detected 6,666 proteins, 2,476 position-specific N-glycosylation sites and 11,929 phosphorylation sites across all 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