Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/sdrf.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/peptides.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/proteinGroups.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/summary.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/mqpar.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/90_NCLPOTr1_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/91_NCLPOTr2_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/88_NCLAOTr2_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/89_NCLAOTr3_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/88_NCLAOTr2_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/87_NCLAOTr1_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/91_NCLPOTr2_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/89_NCLAOTr3_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/92_NCLPOTr3_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/91_NCLPOTr2_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/89_NCLAOTr3_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/92_NCLPOTr3_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/87_NCLAOTr1_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/92_NCLPOTr3_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/88_NCLAOTr2_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/90_NCLPOTr1_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/87_NCLAOTr1_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/90_NCLPOTr1_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063670/uniprotkb_proteome_UP000005640_AND_revi_2023_07_18.fastaprimaryOK200per.artursson@uu.seAlina MeyerData-dependent acquisitionMass SpectrometryBottom-up proteomicshttps://www.ebi.ac.uk/pride/archive/projects/PXD063670Epithelial CellKidneyThe cryopreserved cell samples were thawed and lysed in 25 mM HEPES buffer, pH 7.6, containing 4% sodium dodecyl sulfate and 1 mM DTT. Proteins in the lysate were denatured at 95 °C for 5 min. Samples were prepared for proteomic analysis using a modified sp3 protocol, where simultaneous proteolytic overnight digestion was performed with endoproteinase LysC (FUJIFILM Wako Pure Chemical Corporation, Richmond, USA) and trypsin (Promega, Madison, USA). Protein and peptide amounts were determined by fluorometric quantification using the Protein Broad Range Assay on the Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, USA). Peptides were separated on an EASY-spray C18-column (50 cm, 75 μm inner diameter; Thermo Fisher Scientific, Waltham, USA), using an acetonitrile/water gradient (0.1% formic acid) at 300 nL/min. Eluted peptides where analysed using the TopN method (full MS followed by ddMS2 scans) on an Orbitrap Q Exactive HF mass spectrometer (Thermo Fisher Scientific, Waltham, USA), operating in a data dependent mode with survey scans at a resolution of 120,000, AGC target of 3 x 106 and maximum injection time of 120 ms. The top 15 most abundant isotope patterns were selected from the survey scan with an isolation window of 1.7 m/z and fragmented with nCE at 26. The MS/MS analysis was performed with a resolution of 30,000, AGC target of 1 x 105 and maximum injection time of 50 ms. Each sample was injected in triplicate. The experimental metadata has been generated using lesSDRF.PrideThe raw MS data files were processed with MaxQuant version 2.4.2.0 (https://www.maxquant.org/), where proteins were identified by searching MS and MS/MS data of peptides against a reference human proteome database retrieved from the UniProtKB/Swiss-Prot curated database on 2023-07-18. Carboamidomethylation was set as fixed modification and oxidation and acetylation as variable modifications.ProteomicsPer ArturssonProfessor at Department of Pharmacy, Drug Delivery, Uppsala UniversityPARTIALHomo Sapiens (human)alina.meyer@farmaci.uu.se10.1111/BPH.70493Department of Pharmacy, Uppsala UniversitySwedenfalseIdentification of drug repurposing candidates for the treatment of polycystic kidney disease - RPTEC/TERT1 proteomeAutosomal dominant polycystic kidney disease (ADPKD) is a leading cause of end-stage renal disease with limited treatment options. Drug repurposing offers a promising strategy to find effective treatments. We identified birinapant, bardoxolone methyl and salicylic acid as repurposing candidates for ADPKD and applied thermal proteome profiling to identify disease-relevant targets. Our results uncovered shared effects between the three drugs, including a thermal shift in ADP/ATP translocases (SLC25A4/5/6) caused by reduced ATP production. As expected, salicylic acid displayed a polypharmacological profile but also engaged enzymes along the N-linked glycosylation pathway and inhibited PTK2, an activator of the proliferative PI3K/Akt/mTOR pathway. Orthogonal assays and computational modelling confirmed these findings and located the binding site (499-504) of salicylic acid within PTK2’s ATP-binding pocket. Engagement of several targets was achieved at clinically relevant concentrations.We have identified novel targets of three repurposing candidates that contribute to the cyst growth reducing effects in preclinical ADPKD models and identify salicylic acid, the metabolite of aspirin, as the repurposing candidate with the most promising mechanisms of action.This dataset contains files from the global protein analysis of RPTEC/TERT1 cells cultured on TC-inserts under physiological (10%; PO) and atmospheric (21%; AO) oxygen tension.2026-05-182025-05-06PXD063670NEWT:1773NEWT:3555NEWT:1182590NEWT:10090NEWT:749200NEWT:35554NEWT:4120NEWT:5693NEWT:347515NEWT:1216979NEWT:307972NEWT:92867NEWT:990346NEWT:544496NEWT:5334NEWT:145953NEWT:284812NEWT:115104NEWT:43330NEWT:67825NEWT:44544NEWT:13076NEWT:544404NEWT:3702NEWT:8839NEWT:4232NEWT:1736309NEWT:4113NEWT:7227NEWT:11298NEWT:885318NEWT:876138NEWT:4081NEWT:554NEWT:5691NEWT:260710NEWT:106592NEWT:237561NEWT:9913NEWT:10036NEWT:4100NEWT:7574NEWT:1351NEWT:1076NEWT:6763NEWT:7215NEWT:380394NEWT:272563NEWT:1639NEWT:188229NCBITaxon:79857NEWT:746360NEWT:6239NEWT:135588NEWT:135622NEWT:6915NEWT:9986NEWT:101510NEWT:3880NEWT:58002NEWT:9103NEWT:4577NEWT:146479NEWT:1000589NEWT:145943NEWT:85962NEWT:160488NEWT:317447NEWT:3635NEWT:7955NCBITaxon:2NEWT:7959NEWT:2261NEWT:3197NEWT:9615NEWT:884019NEWT:4565NEWT:1264690NEWT:169963NCBITaxon:38727NEWT:36329NEWT:34305NEWT:59729NCBITaxon:183674NEWT:626528NEWT:139927NEWT:4558NEWT:9606NEWT:367830NEWT:243230NEWT:931281NEWT:7029NEWT:1283300NEWT:334747NEWT:470NCBITaxon:79824NCBITaxon:4563NEWT:3218NEWT:5759NEWT:9838NCBITaxon:9615NEWT:1736231NEWT:1193501NEWT:6287NEWT:6326NEWT:9796NEWT:2762NEWT:5476NEWT:562NEWT:260707NEWT:287NEWT:10117NEWT:10116NEWT:1280NEWT:1836NEWT:29760NEWT:260705NEWT:1148NEWT:4932NEWT:70448NEWT:9825NEWT:3603NEWT:698936NEWT:39946NEWT:11676NEWT:9823NEWT:100226NCBITaxon:6073NEWT:4896NEWT:6279NEWT:7370NEWT:573NEWT:6282NEWT:7091https://orcid.org/0009-0000-2097-6295