{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073074/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073074/C1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073074/C2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073074/S1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073074/S3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073074/C3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073074/S2.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD073074/protein.groups.intensity.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["yctian97s@sjtu.edu.cn"],"submitter":["yuchen tian"],"technology_type":["Mass Spectrometry","Data-independent acquisition"],"software":[""],"submitter_keywords":["Mitochondria","Semaglutide","C2c12"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073074"],"tissue":["Cell Culture"],"sample_protocol":["To isolate enough mitochondria, the C2C12 were cultured in a 15 cm dish. Collect cells at 90% fusion. Mitochondria were isolated using a mammalian cell mitochondrial isolation kit (ThermoFisher, 89874). In short, cell pellets containing 2 × 107 cells were suspended in 800 μl lysis buffer, incubated on ice for 5 minutes, vortexed at maximum speed per minute, and then centrifuged at 700 g at 4 ℃ for 10 minutes. The supernatant was centrifuged at 12000 g for 15 minutes at 4 °C. Then the mitochondrial pellets were rinsed and centrifuged at 12000 g for 5 minutes at 4 °C."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["1. Low-Abundance Enrichment Add 40 μL of EN-Binding Buffer to 40 μL of plasma sample and mix thoroughly. Incubate the mixture at 1500 rpm at room temperature for 5 minutes. Then add 20 μ L of Enrichment Nanobeads, mix well, and incubate at 1500 rpm at room temperature for 1 hour.Add 180 μL of EN-Wash Buffer to the centrifuge tube, mix thoroughly, and place on a magnetic stand. Allow to stand for 3 minutes until magnetic capture is complete. Discard the supernatant. Repeat this procedure 2-3 times. 2 Protein Digestion 1)Add 20 μL of Digestion Buffer 1, then incubate at 1500 rpm and 55°C for 0.5 hours. 2)After incubation, briefly centrifuge the samples and allow them to recover to room temperature. Add 20 μL of dissolved Rapid Trypsin to the samples, then incubate at 1500 rpm, 37°C, protected from light for 2 hours. 3)Add 20 μ L Ending Buffer to terminate digestion. Gently vortex to mix, then place on a magnetic stand and let stand for 3 minutes until complete magnetic separation. Transfer the supernatant for desalting (approximately 60 μL). 3 Solvent Exchange 1) Add 200 μL Activating Buffer to the C18 desalting tip. Place the desalting tip in a centrifuge and centrifuge at 1200 × g for 3 min at room temperature. Discard the Activating Buffer. 2) Add 200 μL Wash Buffer to the desalting tip. Place the desalting tip in a centrifuge and centrifuge at 1200 × g for 3 min at room temperature. Discard the Wash Buffer. 3) Add 60 μL of the sample to be desalted to the desalting tip treated in the above steps. Centrifuge at 1200 × g for 3 min at room temperature. Discard the collected liquid. 4) Add 100 μL Wash Buffer to the desalting tip. Centrifuge at 1200 × g for 3 min at room·temperature. Discard the Wash Buffer. Repeat this step twice. 5) Add 50 μL of Elution Buffer to the desalting tip. Centrifuge at 1200 × g for 3 min at room temperature. Collect 50 μL of Elution Buffer. 6) Add 50 μL Elution Buffer to the desalting tip. Place the desalting tip in a centrifuge and centrifuge at 1200 × g for 3 min at room temperature. Collect a total of 100 μL Elution Buffer using the centrifuge tube from the previous step. 7) Add 50 μL Elution Buffer to the desalting pipette tip. Place the tip in a centrifuge and centrifuge at 1200 × g for 3 min at room temperature. Collect the Elution Buffer in the same centrifuge tube from the previous step, totaling 150 μL. 8) Place the collected elution solution in a vacuum centrifuge concentrator. Centrifuge at 10°C and 1000 rpm for 60 minutes until the liquid is completely dried. Add 25 μL of 1‰ formic acid solution to dissolve the peptide powder. Vortex and centrifuge to ensure complete dissolution 4 Sample Dilution Pipette 1 μL of the reconstituted sample and measure the absorbance at 205 nm using the Nano 300. The peptide concentration (μg/μL) = absorbance at 205 nm /31. Dilute all samples to 0.05 μg/μL. Centrifuge at 16,000 g for 40 minutes. Take 9 μL of the sample and thoroughly mix with 1 μL of iRT. Transfer to the injection vial and prepare for instrument analysis. 5 Instrumentation Methods Separation was performed using the Thermo Scientific Vanquish Neo UHPLC system. A 6 μL sample was injected onto a 150 mm ES906 HPLC column. Separation was achieved via a 13-minute gradient. Peptides separated by liquid chromatography were introduced into the Thermo Orbitrap™ Astral™ Zoom Mass Spectrometers(LC-Bio Technologies (Hangzhou) Co., Ltd.) for DIA (Data Independent Acquisition) in positive ion mode. 6 Protein Database Search Protein search identification and quantitative analysis of the DIA mass spectrometry data were performed using DIA-NN software (https://www.nature.com/articles/s41592-019-0638-x) (version 1.9.2). Key DIA-NN parameters: Protein identification mode set to DirectDIA (eliminating the need for actual DDA data to construct a spectral library; instead, it employs an information-based analysis method to construct a theoretical virtual spectral library from the protein sequence database of the corresponding species). Enzyme digestion parameters set to Trypsin/P, with a maximum missed cleavage count of 2. Fixed modifications: Carbamidomethylation (C). Variable modifications: Oxidation (M), Acetylation (Protein N-terminal). Peptide length range: 7-37. Precursor m/z range: 380-980. Fragment ion m/z range was set to 150-2000, Quantities matrices set FDR threshold to 1, Peptidoforms, MBR, isoform IDs, and protein identification confidence strategy were set to Target-decoy, Protein identification threshold was set to spectrum false positive (PSM FDR) < 0.01, Protein FDR < 0.01."],"omics_type":["Proteomics"],"labhead":["Tian Yuchen"],"instrument_platform":[""],"labhead_affiliation":["Shanghai Sixth People's Hospital, Shanghai"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"submitter_mail":["yctian97s@sjtu.edu.cn"],"publication":["Not available"],"submitter_affiliation":["Shanghai Sixth People's Hospital"],"submitter_country":["China"],"additional_accession":[]},"is_claimable":false,"name":"Semaglutide targets mitochondria to regulate metabolism and inflammation in sarcopenia and osteoarthritis","description":"Metabolic and inflammatory diseases often coexist, and become important challenges facing global health. As a traditional anti-obesity drug, semaglutide is reported to have therapeutic effects in sarcopenia and osteoarthritis (OA), but its mechanism of action still needs to be explored. Here we employed single-cell sequencing analysis to analyze transcriptome changes cross various tissues of high-fat diet (HFD) and OA model mice, and found that semaglutide significantly improved the metabolic and inflammatory disorders of muscle tissue during HFD and OA. Mechanistically, we found that semaglutide could enhance muscle mitochondrial metabolism and mitophagy, alleviated the activation of inflammatory cytokines caused by hypoxia, and regulated the progression of sarcopenia and OA across tissues. Intramuscular injection of mitochondria, pre-stimulated by semaglutide, could significantly alleviate OA inflammation and pain symptoms. These findings reveal the mitochondrial regulatory mechanism in the muscle-OA axis and provide a new perspective for the application of semaglutide in OA treatment.","dates":{"publication":"2026-05-06","submission":"2026-01-14"},"accession":"PXD073074","cross_references":{"TAXONOMY":["NEWT:1773","NEWT:6945","NEWT:3555","NEWT:38783","NEWT:8727","NEWT:1182590","NEWT:8726","NEWT:2","NEWT:157546","NEWT:10090","NEWT:935293","NEWT:749200","NEWT:35554","NEWT:4120","NEWT:5693","NEWT:9417","NEWT:347515","NEWT:8724","NEWT:1216979","NEWT:307972","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:544496","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:5180","NEWT:284812","NEWT:115104","NCBITaxon:1313","NEWT:1081927","NEWT:43330","NEWT:67825","NEWT:44544","NEWT:13076","NEWT:1249668","NEWT:373995","NEWT:544404","NEWT:3702","NEWT:8839","NEWT:317","NEWT:4232","NEWT:990119","NEWT:1736309","NEWT:4113","NEWT:7227","NEWT:11298","NEWT:7469","NEWT:885318","NEWT:171101","NEWT:4081","NEWT:876138","NEWT:554","NEWT:5691","NEWT:98334","NEWT:408170","NEWT:260710","NEWT:3708","NEWT:106592","NEWT:237561","NEWT:9913","NEWT:10036","NEWT:4100","NEWT:7574","NEWT:1351","NEWT:1076","NEWT:6763","NEWT:7215","NEWT:803","NEWT:8030","NEWT:380394","NEWT:272563","NEWT:507601","NEWT:1639","NEWT:188229","NEWT:4909","NCBITaxon:79857","NEWT:95648","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:135588","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:95486","NEWT:3880","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:1911079","NEWT:1000589","NEWT:145943","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:317447","NEWT:3635","NEWT:7955","NCBITaxon:2","NEWT:235443","NEWT:1480154","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:3197","NEWT:9615","NEWT:884019","NEWT:4565","NEWT:1264690","NEWT:169963","NCBITaxon:38727","NEWT:36329","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:243230","NEWT:931281","NEWT:373153","NEWT:7029","NEWT:1283300","NEWT:334747","NEWT:470","NCBITaxon:79824","NCBITaxon:4563","NEWT:3218","NEWT:5759","NEWT:9838","NCBITaxon:9615","NEWT:1736231","NEWT:1193501","NEWT:3055","NEWT:6287","NEWT:2242","NEWT:6326","NEWT:9796","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:29760","NEWT:260705","NEWT:80863","NEWT:1148","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:39946","NEWT:11676","NEWT:9823","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:7370","NEWT:573","NEWT:6282","NEWT:7091","NEWT:1134506"]}}