{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/PPAT-NUDT5_IPMS-Report.tsv"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/checksum.txt"],"Csv":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/sdrf.csv"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-WT_R3_3982.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/293T_R1_3977.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/Sequential_R2_548.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-Y74F_R1_3983.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/Sequential_R1_547.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/293T_R2_3978.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-WT_R1_3980.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-Y74F_R2_3984.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/Sequential_R3_549.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-WT_R2_3981.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-Y74F_R3_3985.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/293T_R3_3979.d.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["mrape@berkeley.edu"],"submitter":["Samuel Witus"],"technology_type":["Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry","Data-independent acquisition"],"software":[""],"submitter_keywords":["Molecular glue","Purine metabolism"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD077951"],"tissue":["Cell Culture"],"sample_protocol":["FLAG-M2 beads from immunoprecipitations were diluted in TNE (50 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA) buffer. RapiGest SF reagent (Waters, 186008090) was added to the mix to a final concentration of 0.1%, and the samples were boiled for 5 min. TCEP was added to 1 mM (final concentration) and the samples were incubated at 37 °C for 30 min. Subsequently, the samples were carboxymethylated with 0.5 mg ml−1 of iodoacetamide for 30 min at 37 °C followed by neutralization with 2 mM TCEP (final concentration). The proteins samples were then digested with trypsin (trypsin:protein ratio, 1:50) overnight at 37 °C. RapiGest was degraded and removed by treating the samples with 250 mM HCl at 37 °C for 1 h followed by centrifugation at 14,000 rpm for 30 min at 4 °C. The soluble fraction was then added to a new tube and the peptides were extracted and desalted using C18 desalting columns (Thermo-Fisher Scientific, PI-87782). Peptides were quantified using BCA assay and a total of 1 μg of peptides were injected for LC-MS analysis.   LC-MS analysis: Trypsin-digested peptides were analyzed by ultra-high-pressure liquid chromatography (UPLC) coupled with tandem mass spectroscopy (LC–MS/MS) using nano-spray ionization. The nanospray ionization experiments were performed using a TimsTOF 2 pro hybrid mass spectrometer (Bruker) interfaced with nanoscale reversed-phase UPLC (EVOSEP ONE). The Evosep method of 30 samples per day was performed using a 10 cm × 150 μm reversed-phase column packed with 1.5 μm C18-beads (PepSep, Bruker) at 58 °C. The analytical columns were connected with a fused silica ID emitter (10 μm inner diameter, Bruker Daltonics) inside a nanoelectrospray ion source (captive spray source, Bruker). The mobile phases comprised 0.1% formic acid as solution A and 0.1% formic acid/99.9% acetonitrile as solution B. The MS settings for the TimsTOF Pro 2 were as follows: the dia-PASEF method for proteomics. The values for mobility-dependent collision energy were set to 10 eV. No merging of TIMS scans was performed. The ion mobility (IM) was set between 0.85 (1/k0) and 1.3 (1/k0) with a ramp time of 100 ms. Each method includes one IM window per dia-PASEF scan with variable isolation window at 20 amu segments; 34 PASEF MS/MS scans were triggered per cycle (1.38 s) with a maximum of 7 precursors per mobilogram. Precursor ions in an m/z range of between 100 and 1,700 with charge states ≥3+ and ≤8+ were selected for fragmentation."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Protein identification, label-free quantification, PTM quantification, and statistical analysis were performed using default settings in Spectronaut 18.0 (Biognosys). The peptide search allowed for two missed cleavages and included phosphorylation (STY) as a variable modification in addition to acetylation and oxidation. Data were mapped to the UniProt reference proteome UP000005640."],"omics_type":["Proteomics"],"labhead":["Michael Rape"],"instrument_platform":[""],"labhead_affiliation":["University of California Berkeley, Howard Hughes Medical Institute"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["witus@berkeley.edu"],"submitter_affiliation":["UC Berkeley"],"submitter_country":["United States"],"additional_accession":[]},"is_claimable":false,"name":"Metabolite glues as a means of purine sensing and chemotherapeutic response","description":"FLAG immunoprecipitation of NUDT5 WT and Y74F, and Strep-FLAG sequential immunoprecipitation of PPAT-NUDT5 complexes from HEK293T cells lentivirally expressing tagged constructs","dates":{"publication":"2026-05-22","submission":"2026-05-03"},"accession":"PXD077951","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: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","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:10029","NEWT:1000589","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","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: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: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:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","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: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:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","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:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:499175","NEWT:476272","NEWT:3747","NEWT:367830","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:28038","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:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:4081","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:2829","NEWT:216599","NEWT:216595","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","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","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:5334","NEWT:37334","NEWT:382352","NCBITaxon:10359","NEWT:242619","NEWT:632957","NEWT:373995","NEWT:5689","NEWT:544404","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:2758385","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:714","NEWT:421932","NEWT:196627","NEWT:5691","NEWT:48479","NEWT:627025","NEWT:1097677","NEWT:61674","NEWT:1117957","NEWT:9913","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:180066","NEWT:135588","NEWT:1843183","NEWT:5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