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Parker"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Tphox","Tmt","C2c12"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD077371"],"sample_protocol":["C2C12 cells were grown in Dulbecco's Modified Eagle Medium, supplemented with 10% fetal bovine serum, pyruvate and GlutaMAX. Cells were kept at 37°C and 5% CO2. At 90% confluence, the cells were differentiated into myotubes with the replacement of 10% FBS with 2% Horse Serum and cultured for a further 3 days. Myotubes were then incubated in 1ml of DMEM, 2% Horse Serum, Pyruvate, GlutaMAX with 0.2% BSA (fatty acid free) with or without 500µM palmitic acid for 24 hours to induce insulin resistance (IR). Relevant cells were then stimulated with 100nM insulin for 30 minutes. Media was removed and cells were washed in cold PBS. Myotubes were then scraped in 10 ml of cold PBS, transferred to a 15 ml falcon tube and spun down at 150 g for 10 minutes at 4 degrees. A stock solution of 50 mM of t-butyl-PhoX (tBu-PhoX) (Thermo Scientific, A52287) resuspended in DMSO was gently heated at 37 degrees Celsius until fully dissolved. Stock solution was then diluted with PBS to 2 mM for tBu-PhoX incubation solution. PBS was removed then removed from the myotubes where the cell pellet was resuspended in 500 µl of PBS containing 2 mM tBu-PhoX and incubated for 30 minutes at room temperature. After incubation, cells were quenched with 10 µl of 1 M Tris pH 8.5 and gently mixed on a shaker for 5 minutes. 10 ml of cold PBS was then added to each sample, cells were spun down at 150 g for 10 minutes at 4 degrees Celsius after which PBS was removed and samples proceeded with lysis for subcellular fractionation. Subcellular fractionation of C2C12 myotubes and EDL muscles was performed using a Subcellular Fractionation Kit (Thermo Scientific; 87790) according to their product protocol. Resulting fractions were labelled with isobaric tags for quantification. Every 1 µg of peptide was labelled with 2 µg of 16-plex tandem mass tags (TMTpro) in 50% acetonitrile at room temperature for 1.5 h (Zecha et al., 2019). The reaction was deacylated with 0.3% (w/v) of hydroxylamine for 10 min at room temperature and quenched to a final volume of 0.1% formic acid (FA) and <5% acetonitrile and pooled. Pooled fractions (4 total) were then loaded onto a HLB-SPE column (Waters Corp; #186008055) pre-conditioned with 1 ml of methanol followed by 1 ml of acetonitrile and finally 2 ml of 0.1% FA. Columns were washed with 2 ml of 0.1% FA and eluted with 1 ml of 80% acetonitrile, 0.1% FA. Phosphopeptides were pre-cleared with 10ul of Fe-NTA Magnetic Agarose beads (Thermo Scientific; A52284) per 500 µg of peptide pre-washed with 1 ml of 80% acetonitrile, 0.1% FA. The unbound flowthrough which contained our protected cross-linked and regular peptides were collected and dried down in a Speedvac at 45 degrees Celsius. The cross-linked/regular peptide flowthrough was resuspended in 100 µl of 0.5% TFA and bath sonicated for 5 minutes. Samples were then shaken at room temperature for 2 hours at 1,800 RPM which deprotected cross-linked peptides. Each sample was diluted to a final concentration of 80% acetonitrile and 0.1% TFA with 400 µl of acetonitrile and transferred to another lo bind tube containing 10ul of Fe-NTA Magnetic Agarose beads (Thermo Scientific; A52284) per 500 µg of peptide pre-washed with 1 ml of 80% acetonitrile, 0.1% TFA. Samples were shaken again for 30 minutes at room temperature at 1,800 RPM to bind deprotected PhoX-modified peptides, after which the unbound flowthrough containing regular peptides only (total proteome) was collected and saved. Beads were washed with 1 ml 80% acetonitrile and 0.1% TFA three times and saved. PhoX-modified peptides were then eluted off the beads twice with 100 µl of 5% ammonium hydroxide shaken at 2000 RPM for 2 minutes at room temperature. The PhoX-modified peptide eluates, as well as regular non-modified peptide fractions for global total proteomic analysis were then loaded onto in-house packed C8 microcolumns to remove any trace agrose beads (3M Empore; #11913614) and centrifuged at 1,000 g and collected in PCR strip tubes. C8 microcolumns were washed with 5 µl of 50% acetonitrile and collected into the same tube to ensure no remaining peptides in the column. Samples were then dried to approximately 50 µl in a Speedvac at 45°C and 200 µl of 99% isopropanol, 1% TFA was added. Peptides were purified by in-house packed SDB-RPS (Sigma; #66886-U) microcolumns and dried by vacuum centrifugation. The PhoX-modified peptides were resuspended in 30% acetonitrile, 0.1% TFA while the non-modified peptides were resuspended in 2% acetonitrile in 0.1% TFA and all samples were stored at -80°C. PhoX-modified peptides were subjected to size exclusion chromatography (SEC) separation as previously described (Harney & Larance, 2023) and 2-3 fractions further separated by by neutral phase C18BEH HPLC into 12 fractions."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["For XL-MS, peptides were analysed on a Dionex 3500 nanoHPLC, coupled to an Orbitrap Eclipse mass spectrometer (ThermoFischer Scientific) via electrospray ionization in positive mode with 1.9 kV at 275 °C and RF set to 30%. Separation was achieved on a 50 cm × 75 µm column packed with C18AQ (1.9 µm; Dr Maisch, Ammerbuch, Germany) (PepSep, Marslev, Denmark) over 20 or 60 min depending on the offline fractionation UV trace at a flow rate of 300 nL/min. The peptides were eluted over a linear gradient of 3–40% Buffer B (Buffer A: 0.1% v/v formic acid; Buffer B: 80% v/v acetonitrile, 0.1% v/v FA) and the column was maintained at 50 °C. The instrument was operated in data-dependent acquisition mode with an MS1 spectrum acquired over the mass range 350–2000 m/z (60,000 resolution, 200% automatic gain control (AGC) and 50 ms maximum injection time) followed by MS/MS via HCD fragmentation with a cycle time of 3 seconds where only peptides with charge state 3-8 were selected with 1.2 m/z isolation window (30,000 resolution, stepped collision energy of 35±8%, 200% AGC, maximum injection time set to 110 ms, enhanced TMTPro resolution mode). XL-MS data were searched against the same skeletal muscle mouse specific proteome database with pLink2 (v2.3.11, Chen et al., 2019). The peptides were searched with oxidation of methionine set as variable modification, and carbamidomethylation of cysteine and TMT to peptide N-termini and Lysine set as a fixed modification set as a fixed modification. Default parameters were used with up to 2 missed cleavages allowed, filter tolerance was set to 10 ppm and peptides were filtered to 1% FDR. XL-MS search was performed using tBu-PhoX as the set linker, where elemental composition was manually imported using cross-linker information from ProteomeDiscoverer."],"omics_type":["Proteomics"],"labhead":["Benjamin Parker"],"instrument_platform":[""],"labhead_affiliation":["The University of Melbourne"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"submitter_mail":["ben.parker@unimelb.edu.au"],"publication":["Not available"],"submitter_affiliation":["The University of Melbourne"],"submitter_country":["Australia"],"additional_accession":[]},"is_claimable":false,"name":"qXL-MS of insulin resistance in C2C12 myotubes","description":"C2C12 myotubes were made insulin resistant with 0.5 mM palmitic acid for 24 h along with non-treated controls and then each group stimulated with or without 100 nM insulin for 30 min (n=4 each). Cells were then cross-linked with 2 mM of tPhoX for a further 30 min in the presence of insulin and the reaction quenched as previously described (Jiang et al., 2022). To increase the depth of analysis, each sample was subjected to a crude biochemical-based separation into four fractions (Wong et al., 2025) followed by digestion with trypsin/LysC. The 16 samples from each fraction were labelled with 16-plex Tandem Mass Tags (TMT) and pooled, followed by the depletion of phosphopeptides and enrichment of XL-peptides using immobilised metal-ion affinity chromatography (IMAC). Each of the four biochemical fractions underwent peptide-level size-exclusion chromatography (SEC) to partially fractionate larger XL-peptides from mono-/loop-linked peptides in 2-3 fractions which were further separated by high pH reversed-phase chromatography into 12 fractions and analysed by LC-MS/MS using data-dependent acquisition (DDA) resulting in the analysis of 132 individual runs. Data were analysed with pLink2 and searched against a skeletal muscle-specific mouse proteome database to limit the search space with filtering to 1% FDR followed by reporter-ion quantification and statistical analysis","dates":{"publication":"2026-05-29","submission":"2026-04-20"},"accession":"PXD077371","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:309807","NEWT:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:43186","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:641809","NEWT:27933","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:79329","NEWT:4442","NEWT:192875","NEWT:1214915","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:60711","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:160621","NEWT:212790","NEWT:931281","NEWT:4432","NEWT:5762","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NEWT:2246","NEWT:2652724","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:4897","NEWT:1148","NEWT:5744","NEWT:5508","NEWT:3329","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1235816","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:2065263","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:1246791","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:7070","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:9483","NEWT:333760","NEWT:1513458","NEWT:1233681","NCBITaxon:40559","NEWT:506599","NEWT:2853422","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:65349","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:109760","NEWT:943274","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:5936","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:55529","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1116234","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:352472","NEWT:1071661","NEWT:1202532","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:1218097","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:153009","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:688333","NEWT:215402","NCBITaxon:548681","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:1034015","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:8694","NEWT:4093","NEWT:4096","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:941442","NEWT:536088","NEWT:13076","NEWT:1226408","NEWT:7108","NEWT:40479","NEWT:43989","NEWT:4076","NEWT:142615","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:4084","NEWT:63577","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8655","NEWT:98351","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:207559","NEWT:407821","NCBITaxon:2","NEWT:85057","NEWT:985076","NEWT:568708","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:267671","NEWT:28532","NEWT:353152","NEWT:8496","NEWT:7165","NEWT:27448","NEWT:40674","NEWT:1194669","NEWT:243230"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