Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20231212_103821_20231212_Coll144_Report_NOTnormalized.log.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/readme.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20231212_103821_20231212_Coll144_Report_NOTnormalized.setup.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_GABARAP-GFP_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_3F_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_LC3-GFP_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_LC3-GFP_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_3F_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_GABARAP-GFP_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_GABARAP-GFP_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_3F_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_LC3-GFP_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20231212_103821_20231212_Coll144.sneftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20231212_103821_20231212_Coll144_Report_NOTnormalized.paramsprimary200OKjoern.dengjel@unifr.chJoern DengjelMass SpectrometryBottom-up proteomicsData-independent acquisitionMap1lc3bLc-ms/msGabarapAutophagyAffinity purificationhttps://www.ebi.ac.uk/pride/archive/projects/PXD048003Samples were digested on beads with trypsin and resulting peptides were purified by STAGE tipps prior DIA-based LC-MS/MS analysis which was performed on a QExactive HFX mass spectrometer coupled to an EasyLC 1000 nanoflow-HPLC (all Thermo Scientific). Peptides were separated on a fused silica HPLC-column tip (I.D. 75 μm, New Objective, self-packed with ReproSil-Pur 120 C18-AQ, 1.9 μm (Dr. Maisch) to a length of 20 cm) using a gradient of A (0.1% formic acid in water) and B (0.1% formic acid in 80% acetonitrile in water): samples were loaded with 0% B with a flow rate of 600 nL/min; peptides were separated by 5%–30% B within 85 min with a flow rate of 250 nL/min. Spray voltage was set to 2.3 kV and the ion-transfer tube temperature to 250°C; no sheath and auxiliary gas were used. The mass spectrometer was operated in the data-independent mode; after each survey scan (mass range m/z = 350 – 1,200; resolution: 120,000) 28 DIA scans with an isolation width of 30.4 m/z were performed covering a total range of precursors from 350-1,200 m/z. AGC target value was set to 3 x 106, resolution to 30,000 and normalized stepped collision energy to 25.5%, 27% and 30%.PrideNot availableThe MS raw files were analyzed using Spectronaut software version 18 and directDIA+ workflow with standard settings using a Uniprot full-length human database and common contaminants such as keratins and enzymes used for digestion as reference.ProteomicsJoern DengjelDepartment of Biology, University of Fribourg Chemin du Musée 10, 1700 Fribourg, Switzerland T +41 26 300 8631PARTIALHomo Sapiens (human)joern.dengjel@medizin.uni-freiburg.de10.1083/jcb.202411213University of FribourgSwitzerlandfalseATG8 interactions in pexophagy conditionsIn the project «ATG8 interactions in pexophagy conditions» anti-GFP affinity purifications (APs) of cells expressing (a) GFP as negative control, (b) GFP-GABARAP, (c) GFP-MAP1LC3B (LC3) were performed (each n=3 biol. replicates).2026-09-142023-12-20PXD048003NEWT:1773NEWT:3555NEWT:38783NEWT:8727NEWT:1182590NEWT:8726NEWT:2NEWT:157546NEWT:10090NEWT:935293NEWT:749200NEWT:35554NEWT:4120NEWT:5693NEWT:9417NEWT:347515NEWT:8724NEWT:1216979NEWT:307972NEWT:92867NEWT:8723NEWT:990346NEWT:544496NEWT:5334NEWT:145953NEWT:257309NEWT:5180NEWT:284812NEWT:115104NCBITaxon:1313NEWT:1081927NEWT:43330NEWT:67825NEWT:44544NEWT:13076NEWT:1249668NEWT:373995NEWT:544404NEWT:3702NEWT:8839NEWT:376741NEWT:4232NEWT:990119NEWT:1736309NEWT:4113NEWT:7227NEWT:11298NEWT:7469NEWT:885318NEWT:171101NEWT:4081NEWT:876138NEWT:554NEWT:5691NEWT:98334NEWT:408170NEWT:260710NEWT:3708NEWT:106592NEWT:237561NEWT:9913NEWT:10036NEWT:4100NEWT:7574NEWT:1351NEWT:1076NEWT:6763NEWT:7215NEWT:3498NEWT:803NEWT:8030NEWT:380394NEWT:272563NEWT:507601NEWT:1639NEWT:188229NEWT:4909NCBITaxon:79857NEWT:95648NEWT:746360NEWT:6239NEWT:1589NEWT:135588NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:95486NEWT:3880NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:1911079NEWT:1000589NEWT:145943NEWT:1902NEWT:85962NEWT:160488NCBITaxon:620NEWT:317447NEWT:3635NEWT:7955NCBITaxon:2NEWT:235443NEWT:985076NEWT:7959NEWT:2261NEWT:623NEWT:3197NEWT:9615NEWT:884019NEWT:4565NEWT:1264690NEWT:169963NCBITaxon:38727NEWT:36329NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:9606NEWT:367830NEWT:157295NEWT:243230NEWT:931281NEWT:373153NEWT:7029NEWT:1283300NEWT:334747NEWT:470NCBITaxon:79824NCBITaxon:4563NEWT:3218NEWT:5759NEWT:9838NCBITaxon:9615NEWT:1736231NEWT:1193501NEWT:6287NEWT:2242NEWT:6326NEWT:9796NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:260707NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:29760NEWT:260705NEWT:80863NEWT:1148NEWT:4932NEWT:70448NEWT:9825NEWT:3603NEWT:698936NEWT:2759NEWT:39946NEWT:11676NEWT:9823NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:7370NEWT:573NEWT:6282NEWT:7091NEWT:11345060000-0002-9453-4614