{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1.pr_matrix.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1.pg_matrix.tsv"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1-HELsh-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1-HEL-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1-HELsh-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1-HEL-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1-HELsh-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1-HEL03-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1-HEL03-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1-HEL-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/YAS202412200028-1-HEL03-2.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065708/uniprot_Homo_sapiens_204318_20240108.fasta"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["jingy@tongji.edu.cn"],"submitter":["Mei Husheng"],"technology_type":["Mass Spectrometry","Top-down proteomics"],"disease":["Acute Leukemia"],"software":[""],"submitter_keywords":["Jak2-v617f，human cell，lc-ms"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD065708"],"tissue":["Blood Cell"],"sample_protocol":["This experiment utilizes a technology platform based on the Ultimate 3000 nano ultra-high-performance liquid chromatography coupled with the Q Exactive Plus high-resolution mass spectrometer, combined with database search software, to perform qualitative (or relative quantitative) analysis of proteins in samples from different experimental groups. The protein list obtained from the experiment reflects the types and relative abundances of proteins detected in this mass spectrometry analysis. Sample processing protocol*(50 to5000 characters) 2.2.1 Enzymatic Digestion Procedure: 1)Transfer the excised protein bands into a 1.5 mL imported centrifuge tube and rinse twice with ultrapure water. 2)Add destaining solution and destain for 30 minutes (until completely destained). 3)Remove the destaining solution and add dehydration solution 1, dehydrate for 30 minutes. 4)Remove dehydration solution 1, add dehydration solution 2, dehydrate for 30 minutes, and then freeze-dry under vacuum. 5)Add 50 μL of reduction solution 1 to the freeze-dried gel pieces and incubate at 55°C for 1 hour. 6)Remove the liquid, cool to room temperature, add 50 μL of reduction solution 2, and keep in the dark for 30 minutes. 7)Remove the liquid and add swelling solution for 10 minutes. 8)Remove the swelling solution and add dehydration solution 1, dehydrate for 30 minutes. 9)Remove dehydration solution 1, add dehydration solution 2, dehydrate for 30 minutes. 10)Remove dehydration solution 2, add 10 μL of digestion working solution, and allow to swell for 30 minutes. 11)Add 20 μL of digestion overlay solution and digest in a water bath at 37°C for 16 hours. 12)Transfer the supernatant after digestion to a new centrifuge tube. 13)Add 50 μL of peptide extraction solution to the remaining gel, incubate in a water bath at 37°C for 20 minutes, centrifuge at 5000g for 5 minutes, combine the supernatants, and repeat the above steps once more. After evaporation, proceed to desalting.  2.2.2 Peptide Desalting Procedure: 1)Prepare a C18 membrane-packed column. 2)Redissolve the dried peptide sample in Nano-HPLC Buffer A. 3)Activation: Pass 40 μL of methanol through the column by centrifugation once, discard the liquid at the bottom of the EP tube, and repeat twice. 4)Equilibration: Pass 40 μL of Nano-HPLC Buffer A through the column by centrifugation once, discard the liquid at the bottom of the EP tube, and repeat twice. 5)Peptide binding: Pass the peptide sample through the column by centrifugation once, then pass the liquid from the bottom of the EP tube through the column again. 6)Desalting: Pass 40 μL of Nano-HPLC Buffer A through the column by centrifugation once, discard the liquid at the bottom of the EP tube, and repeat twice. 7)Elution: Replace with a new EP tube, pass 40 μL of elution phase Buffer B through the column by centrifugation once, collect the liquid at the bottom of the EP tube, and repeat once. 8)Dry down the 80 μL of elution phase Buffer B containing the desalted peptide sample.  2.2.3 Mass Spectrometry and Chromatography Operations: The analytical instrument used in this experiment is a liquid chromatography-tandem mass spectrometry (LC-MS/MS) system consisting of an Ultimate 3000 nano ultra-high-performance liquid chromatograph coupled with a Q Exactive Plus high-resolution mass spectrometer. 1)Redissolve the dried peptide sample in Nano-HPLC Buffer A. 2)Separation is performed using the Nano-HPLC system UltiMate 3000 RSLCnano (ThermoFisher Scientific). Mobile phase A is 0.1% formic acid in water, and mobile phase B is 0.1% formic acid in acetonitrile. The trap column, 100 μm × 20 mm (RP-C18, Agilent), is equilibrated with 100% mobile phase A at a flow rate of 3 μL/min. 3)The sample is loaded by an autosampler and bound to the trap column, followed by separation on an analytical column, 75 μm × 150 mm (RP-C18, New Objective, USA), at a flow rate of 300 nL/min. A blank solvent gradient is used to wash the system for 30 minutes between samples. 4)The enzymatic digestion products are separated by capillary high-performance liquid chromatography and then analyzed using the Q-Exactive Plus mass spectrometer (ThermoFisher Scientific). Detection method: Calibrate the instrument with standard calibration solution before use. Parent ion scan range: 300-1500 m/z. The mass spectrometry scan mode is Data-Dependent Acquisition (DDA), where the 20 most intense fragment spectra (MS2 scan) are acquired after each full scan. Fragmentation method: High-energy Collision Dissociation (HCD) with a normalized collision energy (NCE) of 28. Dynamic exclusion time: 25 seconds. MS1 resolution is set to 70,000 at m/z 200, with an AGC target of 3e6 and a maximum injection time of 100 ms. MS2 resolution is set to 17,500, with an AGC target of 1e5 and a maximum injection time of 50 ms."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["Mass Spectrometry Data Analysis Parameters Proteomic data were processed and analyzed using Proteome Discoverer software (version 2.5, Thermo Fisher Scientific). The MS/MS spectra were searched against the UniProt human-reviewed database (release 2023_02, taxonomy ID 9606) using the following parameters: Mass tolerance: Precursor ion mass tolerance: 10 ppm Fragment ion mass tolerance: 0.05 Da Enzymatic digestion: Maximum missed cleavages: 2 Enzyme: Trypsin Post-translational modifications: Static modification: Carbamidomethylation of cysteine residues Dynamic modifications: Acetylation of protein N-termini Deamidation of asparagine and glutamine residues Oxidation of methionine residues  This configuration allows for comprehensive identification and quantification of peptides and proteins while accounting for common biological modifications and potential digestion artifacts. The use of a reviewed human proteome database ensures high-confidence protein identification with minimized false discovery rates."],"omics_type":["Proteomics"],"labhead":["Jing Yang"],"instrument_platform":[""],"labhead_affiliation":["Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["hsmei@mail.ustc.edu.cn"],"publication":["41332324 Mei H, Wen W, Zhang W, Zhang S, Sun T, Li G, Zhang J, Qi S, Zhou J, Li B, Zhao Y, Chen X, Li B, Xue Y, Lu W, Sun Y, Wang J, Shan H, Zhang S, Huang Y, Chen Y, Wang W, Liu Q, Lu W, Tan L, Ding Y, Fu J, Long J, Zhang L, Zhao B, Liang A, Jiang B, Yang J. Targeting DESI2 as a Novel Therapeutic Strategy for JAK2-Mutant Leukemias. Adv Sci (Weinh). 2026 13(7):e15127 10.1002/advs.202515127"],"submitter_affiliation":["Tongji university"],"submitter_country":["China"],"pubmed_abstract":["The JAK2-V617F mutation is the most common genetic alteration in myeloproliferative neoplasms (MPN), which can progress to secondary acute myeloid leukemia (sAML), a chemotherapy-resistant disease with limited treatment options and a poor prognosis. Although the JAK1/2 inhibitor Ruxolitinib is clinically approved, its efficacy is limited by toxicity to normal cells and the development of drug resistance. Here, the deSUMOylase DESI2 is identified as a novel component of the JAK2-V617F complex by mass spectrometry-based proteomics. Mechanistically, DESI2 selectively binds to and stabilizes JAK2-V617F by mediating its deSUMOylation and deubiquitination at lysine 962 (K962). Importantly, DESI2 protein is specifically and highly expressed in JAK2-mutant-driven cell lines and MPN primary clinical samples, suggesting its potential role in JAK2-V617F regulation and disease progression. Genetic depletion of DESI2 suppresses both JAK2 mutant cell growth and MPN disease onset in vitro and in vivo. Moreover, through a compound screen, followed by chemical proteomics and compound optimization, WWQ-03-012 is discovered, which selectively degrades mutant JAK2, induces primary leukemia cells death, and inhibits MPN progression through targeting DESI2 enzymatic activity in vitro and in vivo. These studies provide a novel therapeutic strategy against mutated JAK2 signaling in MPN and sAML."],"pubmed_title":["Targeting DESI2 as a Novel Therapeutic Strategy for JAK2-Mutant Leukemias."],"pubmed_authors":["Mei Husheng H, Wen Wuqiang W, Zhang Wenjun W, Zhang Shujing S, Sun Ting T, Li Guiming G, Zhang Jing J, Qi Shuang S, Zhou Jie J, Li Bing B, Zhao Yunshuo Y, Chen Xiaotong X, Li Bowen B, Xue Yiying Y, Lu Wang W, Sun Yanli Y, Wang Jingyao J, Shan Hengyue H, Zhang Shengzhe S, Huang Yushan Y, Chen Yisa Y, Wang Wenchao W, Liu Qingsong Q, Lu Wenchao W, Tan Li L, Ding Yi Y, Fu Jianfei J, Long Jun J, Zhang Lei L, Zhao Baobing B, Liang Aibin A, Jiang Baishan B, Yang Jing J"],"additional_accession":[]},"is_claimable":false,"name":"LC-MS-Based Quantitative Proteomic Profiling Reveals WWQ-03-012-Induced Alterations in Protein Expression of Human HEL Cells","description":"This experiment employs an analytical platform based on the Ultimate 3000 nano ultra-high-performance liquid chromatography system coupled to the Q Exactive Plus high-resolution mass spectrometer, combined with database search software, to conduct qualitative (or relative quantitative) analysis of proteins in samples from different experimental groups. The resulting protein list reflects the types and relative abundances of proteins detected in this mass spectrometry analysis.","dates":{"publication":"2026-02-09","submission":"2025-07-03"},"accession":"PXD065708","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:35554","NCBITaxon:12939","NEWT:32046","NEWT:544496","NEWT:59529","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:10245","NEWT:55153","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:351581","NEWT:43186","NEWT:428146","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:661410","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:383379","NEWT:1401257","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:641809","NEWT:27933","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7719","NEWT:7959","NEWT:2261","NEWT:868565","NEWT:31156","NEWT:3112","NEWT:79329","NEWT:4442","NEWT:192875","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:284218","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:160621","NEWT:212790","NEWT:931281","NEWT:4432","NEWT:5762","NEWT:5763","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NEWT:29058","NCBITaxon:79824","NEWT:2246","NEWT:2652724","NEWT:5757","NEWT:68415","NCBITaxon:4563","NEWT:5755","NEWT:44688","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:347256","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:145458","NEWT:633149","NEWT:1149786","NEWT:10239","NEWT:68895","NEWT:44685","NEWT:161934","NEWT:4897","NEWT:1148","NEWT:5744","NEWT:72901","NEWT:213863","NEWT:5508","NEWT:3329","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","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:177437","NEWT:1772","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:11988","NEWT:284812","NEWT:8175","NEWT:400667","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:1245466","NEWT:243277","NEWT:1246791","NEWT:7067","NEWT:118694","NEWT:586722","NEWT:2850","NEWT:118691","NEWT:34871","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:1510","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1303443","NEWT:333760","NEWT:56636","NEWT:1513458","NEWT:1233681","NCBITaxon:40559","NEWT:506599","NEWT:2853422","NEWT:81077","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:65349","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NEWT:34613","NCBITaxon:4932","NEWT:109760","NEWT:29031","NEWT:943274","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:5936","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:886559","NEWT:3750","NEWT:55521","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:1130798","NEWT:55529","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1116234","NEWT:561007","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:203696","NEWT:352472","NEWT:97441","NEWT:1071661","NEWT:1202532","NEWT:360094","NEWT:1408223","NEWT:470","NEWT:1408224","NEWT:41364","NEWT:5911","NEWT:1313","NEWT:1218097","NEWT:1080348","NCBITaxon:50557","NEWT:1314","NEWT:39251","NEWT:39491","NEWT:212142","NCBITaxon:5811","NEWT:29491","NEWT:101841","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:153009","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:688333","NEWT:215402","NCBITaxon:548681","NEWT:318586","NCBITaxon:5820","NEWT:1547","NEWT:272634","NEWT:198107","NEWT:9031","NEWT:27292","NEWT:1872122","NEWT:1308","NEWT:7091","NEWT:1034015","NEWT:760568","NEWT:141262","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:97477","NEWT:7111","NEWT:347515","NEWT:172269","NEWT:9534","NEWT:6269","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:8694","NEWT:4093","NEWT:33936","NEWT:4096","NEWT:8692","NEWT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