{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077984/checksum.txt"],"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077984/F153236.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077984/F154206.xml"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077984/108133030coel_3-GAp15_wt.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077984/110273887coe_ATG16L1.raw"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077984/F153236.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD077984/F154206.mgf"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["dmglover@caltech.edu"],"submitter":["Agata Malinowska"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"software":[""],"submitter_keywords":["Atg16l1; arhgap15; rac1; autophagy; centrosomes; mouse embryonic fibroblasts; pulldown; mass spectrometry","autophagy","Atg16l1","rac1","centrosomes","mass spectrometry","arhgap15","mouse embryonic fibroblasts","pulldown"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD077984"],"sample_protocol":["Flash-frozen cell pellets were thawed on ice at 4 °C and resuspended in 1 ml cell lysis buffer containing 10 mM Tris-HCl, pH 7.2, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Triton X-100 and 10% glycerol. The buffer was freshly supplemented with Benzonase, diluted 1:1000 (Sigma/Millipore, #E1014), 1 mM PMSF and cOmplete EDTA-free protease inhibitor cocktail (Sigma/Millipore, #4693132001). The resuspension was sonicated at 20 kHz for no longer than 30 s and centrifuged at 700 × g for 15 min at 4 °C. The same lysis buffer was used as the washing buffer for all immunoprecipitation assays. The supernatant was transferred to a fresh tube, and the pellet was discarded. For immunoprecipitation of C-terminally tagged ARHGAP15, anti-FLAG magnetic agarose beads (Pierce/Thermo Fisher Scientific, #A36797) or Myc-Trap® Magnetic Agarose beads (Chromotek, #ytma) were equilibrated with lysis buffer according to the manufacturers' instructions. For EGFP::ATG16L1 precipitation, GFP-Trap magnetic agarose beads (Chromotek, #gtma) were used. Beads were diluted in lysis buffer to 1 mg/ml, and 50 µl of bead suspension was used per sample. The protein–bead mixture was incubated on a rotary shaker overnight at 4 °C. Cysteines were reduced by 1 hour incubation with 20 mM tris(2-carboxyethyl)phosphine (TCEP) at 60oC followed by 10 min incubation at a room temperature with 50 mM methyl methanethiosulfonate (MMTS). Digestion was provided at 37°C overnight with 1 µg of trypsin (Promega). After digestion, peptides were eluted from the beads by using a magnet. Pulled aliquots were dried in SpeedVac and re-suspended in an extraction buffer (0.1% TFA 2% acetonitrile) with sonication.   The next step was processed using single-pot solid-phase-enhanced sample preparation (SP3). Magnetic beads mix were prepared by combining equal parts of Sera-Mag Carboxyl hydrophilic and hydrophobic particles (09-981-121 and 09-981-123, GE Healthcare). The bead mix was washed three times with MS-grade water and re-suspended in a working concentration of 10 µg/µl. The bead mix was then added to the samples then suspended in 100% acetonitrile, this step was repeated 3 times. Pure peptides ware eluted from the beads by using 2% acetonitrile  in MS-grade water. Using a magnet, the peptides solution was separated from beads. Peptide mixture was dried in SpeedVac and re-suspended in 80 µl extraction buffer (0.1% TFA 2% acetonitrile) with sonication.   20 µl of peptide mixture was analysed using LC-MS system composed of Evosep One (Evosep Biosystems, Odense, Denmark) coupled to a Orbitrap Exploris 480 mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) via Flex nanoESI ion source (Thermo Fisher Scientific, Bremen, Germany). Samples were loaded onto disposable Evotips C18 trap columns (Evosep Biosystems, Odense, Denmark) according to the manufacturer protocol with minor modifications. Briefly, Evotips were activated with 25 µl of 80% solution solvent B and 20% solvent A (solvent B: 0.1% formic acid in acetonitrile) by 1 min centrifugation at 600 g followed by 2 min incubation in 2-propanol. After equilibration with 25 µl of solvent A, 20 µl of each sample was loaded onto the solid phase. Bound peptides were washed twicewith 50 µl and covered with 200 µl of solvent A. Chromatography was carried out at a flow rate 250 nl/min using the 88 min (15 samples per day) preformed gradient on EV1106 analytical column (Dr Maisch C18 AQ, 1.9 µm beads, 150 µm ID, 15 cm long, Evosep Biosystems, Odense, Denmark). Data was acquired in positive mode with a data-dependent method using the following parameters. MS1 resolution was set at 60 000 with a normalized AGC target 300%, Auto maximum inject time and a scan range of 300 to 1600 m/z. For MS2, resolution was set at 15 000 with a Standard normalized AGC target, Auto maximum inject time and top 40 precursors within an isolation window of 1.6 m/z considered for MS/MS analysis. Dynamic exclusion was set at 20 s with allowed mass tolerance of ±10 ppm and the precursor intensity threshold at 5e3. Precursor were fragmented in HCD mode with normalized collision energy of 30%."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Raw data were pre-processed with Mascot Distiller (version 2.7, Matrix Science Limited) and searched with Mascot Search Engine (version 2.7, Matrix Science Limited) against Mus musculus or Homo sapiens protein sequences derived from Swissprot (version 2021_03, 565,254 sequences or 20,446 sequences, respectively). Other search settings were as follows: enzyme – trypsin, fixed modifications – Methylthio (C), variable modifications – Oxidation (M), peptide mass tolerance – 5 ppm, fragment mass tolerance – 0.01 Da, missed cleavages – 2. Files were re-calibrated offline using results from preliminary searches. FDR was computed with target-decoy strategy implemented in Mascot and kept under 1%."],"omics_type":["Proteomics"],"labhead":["Prof. David M. Glover"],"instrument_platform":[""],"labhead_affiliation":["Biology and Biological Engineering Division, California Institute of Technology, USA"],"submission_type":["COMPLETE"],"species":["Homo Sapiens (human)","Mus Musculus (mouse)"],"submitter_mail":["esme@ibb.waw.pl"],"publication":["Not available"],"submitter_affiliation":["IBB PAS"],"submitter_country":["Poland"],"doi":["10.6019/PXD077984"],"additional_accession":[]},"is_claimable":false,"name":"Identification of the protein network associated with EGFP::ATG16L1 and ARHGAP15::MYC","description":"These datasets contain mass spectrometry-based proteomics results from affinity-purification/pulldown assays designed to identify proteins associated with the autophagy regulator EGFP::ATG16L1 and the RAC1-specific GTPase-activating protein ARHGAP15::MYC. Experiments were performed using mouse embryonic fibroblasts expressing tagged EGFP::ATG16L1 or ARHGAP15::MYC, followed by immunoprecipitation using GFP-Trap or Myc-Trap/anti-tag magnetic agarose beads and LC–MS/MS analysis. The datasets were generated to investigate protein interaction networks linking ARHGAP15, RAC1 signalling, ATG16L1-dependent autophagy and centrosome regulation.","dates":{"publication":"2026-06-18","submission":"2026-05-04"},"accession":"PXD077984","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:1211601","NEWT:876138","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:51329","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:260707","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:105231","NEWT:1216981","NCBITaxon:6073","NEWT:884204","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:38783","NEWT:8727","NEWT:4006","NEWT:8726","NEWT:6426","NEWT:6669","NEWT:10090","NEWT:4120","NEWT:51515","NEW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