Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/PPAT-NUDT5_IPMS-Report.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/sdrf.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-WT_R3_3982.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/293T_R1_3977.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/Sequential_R2_548.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-Y74F_R1_3983.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/Sequential_R1_547.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/293T_R2_3978.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-WT_R1_3980.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-Y74F_R2_3984.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/Sequential_R3_549.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-WT_R2_3981.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/NUDT5-Y74F_R3_3985.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077951/293T_R3_3979.d.zipprimaryOK200mrape@berkeley.eduSamuel WitusAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryData-independent acquisitionMolecular gluePurine metabolismhttps://www.ebi.ac.uk/pride/archive/projects/PXD077951Cell CultureFLAG-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.PrideNot availableProtein 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.ProteomicsMichael RapeUniversity of California Berkeley, Howard Hughes Medical InstitutePARTIALHomo Sapiens (human)Not availablewitus@berkeley.eduUC BerkeleyUnited StatesfalseMetabolite glues as a means of purine sensing and chemotherapeutic responseFLAG immunoprecipitation of NUDT5 WT and Y74F, and Strep-FLAG sequential immunoprecipitation of PPAT-NUDT5 complexes from HEK293T cells lentivirally expressing tagged constructs2026-05-222026-05-03PXD077951NEWT:6945NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:1211601NEWT:876138NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:1351NEWT:1438992NEWT:2649997NEWT:272563NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:3885NEWT:3888NEWT:1589NEWT:135622NEWT:6915NEWT:3649NEWT:101510NEWT:3880NEWT:272559NEWT:3641NEWT:383379NEWT:10029NEWT:1000589NEWT:85962NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:197NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:1270NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:294128NEWT:11676NEWT:55571NEWT:100226NEWT:4530NEWT:4896NEWT:75058NEWT:13616NEWT:1094343NEWT:296543NEWT:1773NEWT:1895NEWT:1182590NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NCBITaxon:1313NEWT:43330NEWT:408169NEWT:44544NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:990119NEWT:408172NEWT:408170NEWT:493760NEWT:260710NEWT:257313NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:1432138NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:9598NEWT:8030NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:432359NEWT:46835NEWT:2711NEWT:376686NEWT:95486NEWT:9103NEWT:29159NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:3635NEWT:5811NEWT:235443NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:499175NEWT:476272NEWT:3747NEWT:367830NEWT:178616NEWT:410289NEWT:373153NEWT:352472NEWT:360094NEWT:470NEWT:1313NEWT:411469NEWT:84023NEWT:559292NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2762NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:28038NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:327159NEWT:178876NEWT:327160NEWT:573NEWT:9031NEWT:7091NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:5180NEWT:256737NEWT:115104NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:13076NEWT:1249668NEWT:317NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:415540NEWT:4081NEWT:554NEWT:98334NEWT:426428NEWT:7574NEWT:7215NEWT:575412NEWT:29204NEWT:2172103NEWT:507601NCBITaxon:6157NEWT:746360NEWT:6239NEWT:470150NEWT:216257NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:435590NEWT:1902NEWT:160488NEWT:28104NCBITaxon:2NEWT:985076NEWT:1215323NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:2829NEWT:216599NEWT:216595NEWT:243230NEWT:8355NEWT:9685NEWT:7029NEWT:1080772NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:260707NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NCBITaxon:6073NEWT:884204NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NEWT:607699NEWT:6282NEWT:208964NEWT:1134506NEWT:575584NEWT:38783NEWT:8727NEWT:4006NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:5334NEWT:37334NEWT:382352NCBITaxon:10359NEWT:242619NEWT:632957NEWT:373995NEWT:5689NEWT:544404NEWT:9925NEWT:8839NEWT:4232NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:196627NEWT:5691NEWT:48479NEWT:627025NEWT:1097677NEWT:61674NEWT:1117957NEWT:9913NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:29722NEWT:380394NEWT:1692259NEWT:180066NEWT:135588NEWT:1843183NEWT:58002NEWT:326423NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:418985NEWT:146479NEWT:1911079NEWT:264203NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:9612NEWT:38865NEWT:51953NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:349741NEWT:9605NEWT:9606NEWT:157295NEWT:641501NEWT:7668NEWT:915099NEWT:74940NEWT:9721NEWT:137221NEWT:1450511NEWT:1143193NEWT:411901NEWT:9838NEWT:105884NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:5476NEWT:1274432NEWT:1274426NEWT:70448NEWT:9825NEWT:1274423NEWT:393765NEWT:698936NEWT:39946NEWT:9823NEWT:9940NEWT:521001NEWT:39947NEWT:1274420NEWT:5784580000-0003-1907-8484