Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_100C_Rep1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_60C_Rep2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_100C_Rep3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_90C_10B_Rep4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_60C_Rep4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_30C_Rep1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_90C_10B_Rep2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_10C_Rep3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_10C_Rep1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_30C_Rep3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_100C_Rep2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_60C_Rep1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_90C_10B_Rep1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_90C_10B_Rep3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_100C_Rep4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_10C_Rep4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_60C_Rep3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_30C_Rep4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_30C_Rep2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex_10C_Rep2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD069688/Exp-M-026_AoU_16plex.mzTabprimaryOK200lars.plate@vanderbilt.eduJake HermansonData-dependent acquisitionAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryBottom-up proteomicsAp-msHypothyroidisimLc-ms/msTmthttps://www.ebi.ac.uk/pride/archive/projects/PXD069688Cell CultureEngineered FRT cells were seeded in 10 cm dishes so that on day of harvest, ~72 hours after seeding, cell plates were >80% confluent. Cells were washed 2 times with 5 mL of PBS followed by adding 5 mL of PBS + 500 μM DSP and incubated at 37 °C for 10 min. An additional 5 mL of 200 mM Tris [pH 7.5] was then added to the cells and incubated at 37 °C for 5 min. Cells were then washed with cold PBS and 500 μL of RIPA +protease inhibitor was added to the plates. Plates were incubated at 4 °C for 30 minutes with gentle rocking. Cell plates were then scraped, and debris was cleared by centrifuging at 14,000 x rpm for 10 min at 4 °C. Protein concentration was normalized to 600 μg of protein in 600 μL using a BCA assay (Thermo Scientific, 23225). Normalized lysates were then mixed end over end for 1 hour at 4 °C with 50 μL of Sepharose 4B bead slurry (MilliPore, 4B200) prewashed with PBS. Samples were then centrifuged at 4 °C for 5 min at 300 x g and the supernatant was collected and transferred to a new tube with 20 μL of pre-equilibrated Pierce anti-FLAG magnetic beads (Thermo Scientific, A36797) and allowed to mix end over end for ~18 hours. The samples were then washed 4 times with 500 μL of RIPA discarding the supernatant each time. The protein was then eluted by adding 100 μL of elution buffer (4% SDS, 100 mM Tris [pH 6.8]) and heating at 95 °C for 5 min. Co-Immunoprecipitation elution was prepared for MS using a single pot, solid phase-enhanced sample preparation (SP3) beads (cytiva, 65152105050250 and 45152105050250) sample processing method previously described that utilizes a Biomek i5.65 Breifly, proteins were first reduced with 5 mM DTT at 60 °C/700 rpm for 30 min then alkylated with 20 mM IAA for 30 min at 21 °C in the dark. Finally, the reaction was quenched with a second addition of 5 mM DTT for 15 min at 21 °C. This protein was then digested on 8 μL of total SP3 beads (1:1 hydrophobic to hydrophilic) in 50 μL of 50 mM HEPES [pH 8] with 0.5 μg of Trypsin/Lys-C (Promega, V5073) for 10 hours at 37 C while shaking at 700 rpm. Sample was kept at 4 °C until further use. The supernatant was transferred to a new tube and had 10 μL of water added. Next 40 μL of TMT reagent resuspended in acetonitrile (Thermo, A44520) was added to the sample and allowed to incubate for 1 hour. After this, 4 μL of freshly made 10% ammonium bicarbonate was added and incubated at room temperature for 1 hour to quench excess TMT reagent. Samples were then pooled and acidified to a pH of less than 2 with formic acid. Sample volume was then reduced to ~800 μL and then brought back up to ~1600 μL with buffer A (94.9% H2O, 5% acetonitrile, 0.1% formic acid). LC-MS/MS data-dependent analysis was performed using an Exploris480 mass spectrometer (Thermo Fisher) equipped with a Dionex Ultimate 3000 RSLCnano system (Thermo Fisher). MudPIT columns were made as previously described with 600 μL of labeled peptides loaded onto the trap column using a high-pressure chamber. To elute peptides from the first C18 phase to the SCX resin of the MudPIT column, 10 μL of Buffer A was injected and the following 90 minute gradient was utilized: 4% B (99.9% acetonitrile, 0.1% formic acid v/v) (5 min hold) ramped to a mobile phase concentration of 40% B over 90 minutes, ramped to 80% B over 5 mins, held at 80% B for 5 mins, then returned to 4% B for 5 mins and then held at 4% B for the remainder of the analysis at a constant flow rate 500 nl/min. Then to fractionate the sample, 10 µL sequential injections of 10, 30, 60, and 100% buffer C (500 mM ammonium acetate in buffer A) in Buffer A, with a final fraction injection of 90% buffer C and 10% buffer B were utilized with a corresponding 130 min gradient at a flow rate of 500 nl/min (4% B for 10 mins then ramped to 40% B over 90 mins, increased to 80% B over 5 mins then held at 80% B for 5 mins and returned to 4% in 5 mins, and held at 4% for the remainder of the analysis). A 3 sec duty cycle was utilized consisting of a full scan (400-1600 m/z, 120,000 resolution) and subsequent MS/MS spectra collected in TopSpeed acquisition mode. For MS1 scans, the maximum injection time was set to 50 msec with a normalized AGC target of 100%. Ions were selected for MS/MS fragmentation based on the following criteria: MS1 intensity above 1e4, charge state between 2-6, and monoisotopic peak determination set to peptide. Additionally, a dynamic exclusion time of 45 secs was utilized (determined from peptide elution profiles) with a mass tolerance of +/- 10 ppm to maximize peptide identifications. MS/MS spectra were collected with a normalized HCD collision energy of 36, 0.4 m/z isolation window, auto selected for maximum injection time mode, a normalized AGC target of 100%, at a MS2 orbitrap resolution of 45,000 with a defined first mass of 110 m/z to ensure measurement of TMTPro reporter ions.PrideProteome Discoverer 2.4 (Thermo Fisher Scientific) was utilized to obtain peptide identifications and TMT-based protein quantification. MS/MS spectra were searched using SEQUEST-HT against a Uniprot SwissProt rat proteome with human Tg manually added (downloaded Aug 27th 2020), contaminant FASTA50 (containing 379 entries), and a decoy database of reversed peptide sequences. Peptide precursor ion mass tolerance was set to 20 ppm, and fragment ion mass tolerance was fixed at 0.02 Da. Only peptides with a minimum length of six amino acids were considered, and trypsin digestion was assumed with a maximum of two missed cleavages allowed. Dynamic modifications included oxidation of methionine (+15.995 Da), protein N-terminal methionine loss (-131.040 Da), protein N-terminal acetylation (+42.011 Da), and a combination of N-terminal methionine loss and acetylation (-89.030 Da). Static modifications were applied for cysteine carbamidomethylation (+57.021 Da) and TMTpro labeling on the N-terminus or lysines (+304.207 Da). To control false discoveries, the peptide-level false discovery rate (FDR) was set to 1% using the percolator algorithm. Quantification of TMT reporter ions was performed by including only those with an average signal-to-noise ratio greater than 10:1 and a co-isolation percentage of less than 25%. TMT reporter ion intensities were summed for peptides assigned to the same protein, including razor peptides, which are shared by multiple proteins but assigned to the one providing the most confident identification. Protein identifications were filtered at a 1% FDR threshold, and protein grouping was conducted according to the parsimony principle, which minimizes the number of protein groups assigned to each peptide. Analysis was subsequently carried out using custom R code available on GitHub (https://github.com/Plate-Lab/). Briefly, median normalization was performed across TMT channels for statistical analysis and determination of purified proteins. Downstream, intensities were bait normalized to Tg within each variant.ProteomicsLars PlateDepartment of Chemistry, Biological Sciences, Microbiolgy and Immunology at Vanderbilt UniversityCOMPLETERattus Norvegicus (rat)Homo Sapiens (human)jake.hermanson@vanderbilt.edu42463052 Hermanson JN, Hudson AD, Plate L. Public Cohort Analysis Identifies Thyroglobulin Variants as Hypothyroidism Risk Factors. J Biol Chem. 2026:113344 10.1016/j.jbc.2026.113344Vanderbilt UniversityUnited States10.6019/PXD069688Hypothyroidism is a prevalent endocrine disorder characterized by insufficient thyroid hormone (T3T4) production. Thyroglobulin (Tg) serves as the prohormone for T3 and T4 production, with many variants of uncertain clinical significance due to genetic diversity in the Tg gene. We leveraged the large-scale All of Us biobank to investigate the disease association of prevalent yet undercharacterized Tg variants. We related variant presence to thyroid-stimulating hormone levels and levothyroxine (LT4) usage as proxies for thyroid function. This identified R152H, Q870H, A993T, P1012L, and P1494L variants linked to increased LT4 usage and decreased thyroid function, while the R320C variant was associated with decreased thyroid function. Molecular characterization in Fisher rat thyroid cells revealed decreased secretion efficiency of R152H, Q870H, and R320C variants. Affinity purification-mass spectrometry demonstrated that secretion-deficient variants showed higher engagement with the protein homeostasis network, indicating protein quality control defects as the pathophysiology mechanism. In contrast, secretion-competent A993T and P1494L variants showed elevated interactions with degradation and antigen-presentation pathways, suggesting an alternative pathophysiology possibly linked to Hashimoto's disease, an autoimmune condition with overproduction of autoantibodies that target thyroid proteins. In support, participants carrying the A993T or P1494L variants had elevated anti-thyroidperoxidase (TPO) antibody levels. We estimate ∼115,000 US individuals currently taking levothyroxine could benefit from precision medicine targeting these variants, with ∼85,000 carrying Q870H. Our findings highlight the power of combining large public biobank data with molecular characterization to understand Tg genotype-to-phenotype relationships. Q870H represents a candidate for molecular therapies to restore secretion, offering precision medicine beyond LT4 replacement therapy.Public Cohort Analysis Identifies Thyroglobulin Variants as Hypothyroidism Risk Factors.Hermanson Jake N JN, Hudson Andrew D AD, Plate Lars LfalsePublic Cohort Analysis Identifies Thyroglobulin Variants as Hypothyroidism Risk FactorsHypothyroidism is a prevalent endocrine disorder that is characterized by the insufficient production of thyroid hormones (T3/T4), with etiologies related to environmental, autoimmune factors, or genetic variants. Thyroglobulin (Tg) serves as the prohormone to T3/T4 production and due to a large genetic diversity there are many variants of clinical uncertainty. Here, we leveraged the large-scale “All of Us” biobank to investigate disease association of Tg variants that are more prevalent in the general population compared to previously characterized variants. We compared these variants to thyroid stimulating hormone levels and levothyroxine (LT4) usage to estimate thyroid function. This identified R152H, Q870H, A993T, P1012L and P1494L variants linked to an increased susceptibility to levothyroxine usage and decreased thyroid function while the R320C variant was associated with a decrease in thyroid function. Molecular characterization and secretion of these variants in Fisher rat thyroid cells showed decreased secretion efficiency and/or correlates with higher anti-TPO antibody levels in participants for disease associated variants while benign variants showed minimal effect. Using previously determined structures of Tg, variants found with a decrease in thyroid efficiency are in structural positions that disrupt stabilizing bonds, but variants with minimal effect are in more flexible regions with fewer interactions. Affinity purification mass spectrometry demonstrated that secretion deficient variants show higher engagement with the protein homeostasis network. We estimate that around 150,000 individuals in the US could benefit from precision medicine with the variants highlighted in this study currently take levothyroxine, with ~100,000 of those individuals carrying the Q870H variant. Our findings highlight the power of combining data from large public biobanks with molecular characterization to better understand the genotype to phenotype relationships of Tg. Our analysis suggests that Q870H serves as a possible candidate to be targeted by molecular therapies to restore secretion and T3/T4 production offering a precision medicine approach beyond LT4 replacement therapy.2026-08-072025-10-21PXD069688NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:475174NEWT:111205NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:656064NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:641809NEWT:38815NEWT:317447NEWT:4688NEWT:111225NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:1912919NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:270643NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:8165NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2709072NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:1185650NEWT:216778NEWT:294607NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:317047NEWT:460523NEWT:235443NEWT:1757312NEWT:85694NEWT:108458NEWT:5936NEWT:320637NEWT:1078283NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:470NEWT:5911NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:166313NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:906914NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:381666NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:9983NEWT:8655NEWT:5147NEWT:28108NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:298176NEWT:40674NEWT:1194669NEWT:51329NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:475932NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:99488NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:29829NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:300273NEWT:4232NEWT:416348NEWT:11298NEWT:4236NEWT:7742NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:563041NEWT:72664NEWT:36599NEWT:41949NEWT:249161NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:29835NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:35231NEWT:8644NEWT:1125630NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:192222NEWT:9963NEWT:1617910NEWT:637379NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:186801NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NEWT:194439NCBITaxon:12637NEWT:38727NEWT:218496NEWT:8618NEWT:70448NEWT:300251NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:2627626NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:54195NEWT:10136NEWT:38942NEWT:4762NEWT:6941NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:8697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