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Jain"],"technology_type":["Mass Spectrometry","Bottom-up proteomics","Data-independent acquisition"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD069668"],"tissue":["Fibroblast"],"sample_protocol":["HCA2-hTert cells were used for all experimnets. For SPROX experiments, the cells were lysed under native condition and then aliquoted into 750ul volumes. Each aliquot was equilibrated at 25 °C for 30 min prior to oxidation, then was oxidized by adding 84 µl of 9.8 M hydrogen peroxide (Fisher), yielding a final peroxide concentration of 0.98 M. Samples were incubated at 25 °C for various time points. Positive controls were oxidized for 120 minutes. Negative controls (0 min) were treated with an equal volume of Milli-Q water. Oxidation reactions were quenched with 834 µl of 2M sodium sulfite, bringing the total reaction volume to 1.7 ml.The quenched lysates were reduced with 6 µl of 1.25 M DTT (Sigma) for 1 hour at room temperature, then alkylated with 167.4 µl of 100 mM IAA (Sigma) for 15 min at room temperature in the dark. The lysates were then adjusted to final concentrations of 2 M urea and 20 mM HEPES by adding 613.8 µl of stock solution. For all samples except the positive controls, this stock solution contained 8 M urea and 80 mM HEPES. For positive controls, which already contained urea from the earlier 5 µg/µl dilution, the stock contained 80 mM HEPES and a proportionally lower urea concentration. Samples were then digested overnight at room temperature in a mixing rotor with trypsin (Pierce) at a 1:37.5 enzyme-to-substrate ratio. Resulting peptides were purified on Sep-Pak C18 cartridges (Waters) according to the PTMScan® HS Ubiquitin/SUMO Remnant Motif (K-ε-GG) Kit protocol. Eluates were frozen, dried by vacuum centrifugation, resuspended in 0.1% TFA, and quantified with a fluorometric peptide assay (Thermo). Peptides were then adjusted to a final concentration of 0.25 µg/µl prior to LC–MS/MS analysis.For non-SPROX experiments, 25 µg of total protein for non-KGG analyses (processed on ProtiFi S-Trap micro columns) and 3.75 mg total protein for KGG analyses (processed on ProtiFi S-Trap midi columns) was used. For both analyses, samples were reduced with 2 mM DTT (Sigma) for 1 h at 55 °C followed by alkylation with 10 mM IAA (Sigma) for 30 min at room temperature in the dark. Samples were acidified with 1.2% phosphoric acid, mixed with six volumes of 90% methanol in 100 mM triethylammonium bicarbonate (TEAB), and loaded onto the S-Trap columns. Columns were centrifuged at 4000 ×g for 1 min and washed twice with 90% methanol in 100 mM TEAB. Bound proteins were digested on-column overnight at 37 °C with trypsin using a 1:25 enzyme-to-substrate ratio for S-Trap micro columns and 1:37.5 for S-Trap midi columns. Peptides were sequentially eluted with 0.1% trifluoroacetic acid (TFA) and 50/50 acetonitrile:0.1% TFA, using equal volumes of each elution buffer (40 µl for S-Trap micro and 195 µl for S-Trap midi). Eluates were then frozen, dried by vacuum centrifugation, and resuspended in 0.1% TFA prior to analysis by LC–MS/MSFor both non-SPROX and SPROX experiments, KGG peptides were selectively enriched using the PTMScan® HS Ubiquitin/SUMO Remnant Motif (K-ε-GG) kit (Cell Signaling Technology), which utilizes magnetic beads conjugated to anti-KGG antibodies. Following enrichment, peptides were desalted using homemade C18 Stage Tips and dried by vacuum centrifugation. For non-SPROX experiments, peptides were resuspended in 15 µl of 0.1% trifluoroacetic acid (TFA). For SPROX experiments, the resuspension volume was adjusted from 10 to 15 µl to account for variable pre-enrichment peptide concentrations as determined by the fluorometric peptide assay (Thermo).Please refer to the methods section of the accompanying manuscript for more detailed sample processing protocol."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Please refer to the methods section of the accompanying manuscript for detailed data processing protocol. Briefly, raw DIA-MS data were analyzed using DIA-NN (v2.2.0) in library-free mode. Predicted spectral libraries were generated in silico from the Homo sapiens reference proteome. Two libraries were constructed: one for global searches (with methionine oxidation as a variable modification; maximum number of variable modifications set to one) and another for KGG-enriched searches (with methionine oxidation and lysine ubiquitination as variable modifications; maximum number of variable modifications set to two).Raw files were searched against the appropriate library with the following parameters: peptide length 7–30 residues, charge states 2–4, precursor m/z 380–980, and fragment m/z 150–2000. Protein N-terminal methionine excision, cysteine carbamidomethylation, re-annotation, contaminant filtering, match-between-runs, and protein inference were enabled. One missed cleavage was allowed.  Mass accuracy was set to 10.0 ppm and MS1 accuracy to 4.0 ppm. Peptidoform level scoring was applied, and all other parameters were left at default values. For isotopic labeling and chloramphenicol experiments, lysine and arginine were defined as SILAC modifications as described in the DIA-NN documentation, and searches were performed against either the global or KGG-enriched library as appropriate. The resulting report.parquet files generated by DIA-NN were used for subsequent analyses. Prior to downstream analyses, data were filtered at the precursor level (q.value ≤ 0.01) and protein level (pg.q.value ≤ 0.01).Quantitation was based on MS2 precursor levels generated by DIA-NN. Fractional labeling was measured by dividing the heavy precursor levels by the sum of heavy and light levels. In measuring methionine oxidation rates, only peptides containing single methionines and no cysteines (in both KGG and non-KGG peptides) were used for downstream analysis. For each peptide, precursor levels were measured as a function of oxidation time. Intensities for each oxidation time point were normalized relative to the fully oxidized and fully unoxidized samples to measure the fraction of proteins that remained unoxidized. The resulting oxidation decay curves were fit to a first-order kinetic model: fraction unoxidized (t)=e^(-k_ox t)Goodness of fit was assessed by calculating the R² values of the least-squares fits. Resulting kox measurements of less than 3 min-1 and greater than 1e-4 min-1 with R2 values of greater than 0.8 were used for all downstream analyses."],"omics_type":["Proteomics"],"labhead":["Sina Ghaemmaghami"],"instrument_platform":[""],"labhead_affiliation":["Ghaemmaghami Lab, Department of Biology, University of Rochester, NY, US"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["anushka.jain@rochester.edu"],"publication":["Not available"],"submitter_affiliation":["University of Rochester"],"submitter_country":["United States"],"additional_accession":[]},"is_claimable":false,"name":"Protein misfolding exposes buried ubiquitination sites that drive rapid proteasomal clearance ","description":"In this study, we combine structural proteomics and time-resolved isotopic labeling to profile the modification sites, dynamics, and conformational properties of the human ubiquitinome.","dates":{"publication":"2026-04-26","submission":"2025-10-20"},"accession":"PXD069668","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:1589","NEWT:135622","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:36630","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:410658","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:491","NEWT:460523","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:1640278","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:10832","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:105487","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:214053","NEWT:28550","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:29829","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:441772","NEWT:48106","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxo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