{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20231212_103821_20231212_Coll144_Report_NOTnormalized.log.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/readme.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20231212_103821_20231212_Coll144_Report_NOTnormalized.setup.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_GABARAP-GFP_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_3F_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_LC3-GFP_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_LC3-GFP_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_3F_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_GABARAP-GFP_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_GABARAP-GFP_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_3F_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20230818_MB_CAR_LC3-GFP_2.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20231212_103821_20231212_Coll144.sne","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD048003/20231212_103821_20231212_Coll144_Report_NOTnormalized.params"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["joern.dengjel@unifr.ch"],"submitter":["Joern Dengjel"],"technology_type":["Mass Spectrometry","Bottom-up proteomics","Data-independent acquisition"],"software":[""],"submitter_keywords":["Map1lc3b","Lc-ms/ms","Gabarap","Autophagy","Affinity purification"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD048003"],"sample_protocol":["Samples 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%."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["The 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."],"omics_type":["Proteomics"],"labhead":["Joern Dengjel"],"instrument_platform":[""],"labhead_affiliation":["Department of Biology, University of Fribourg  Chemin du Musée 10, 1700 Fribourg, Switzerland  T  +41 26 300 8631"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["joern.dengjel@medizin.uni-freiburg.de"],"publication":["10.1083/jcb.202411213"],"submitter_affiliation":["University of Fribourg"],"submitter_country":["Switzerland"],"additional_accession":[]},"is_claimable":false,"name":"ATG8 interactions in pexophagy conditions","description":"In 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).","dates":{"publication":"2026-09-14","submission":"2023-12-20"},"accession":"PXD048003","cross_references":{"TAXONOMY":["NEWT:1773","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:376741","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:3498","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","NCBITaxon:620","NEWT:317447","NEWT:3635","NEWT:7955","NCBITaxon:2","NEWT:235443","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:623","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: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"],"pubmed":[],"ORCID":["0000-0002-9453-4614"]}}