Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_P53_2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_P53_1.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_NEG_3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_NEG_2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_P53_3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_NEG_1.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_NEG_3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_NEG_1.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_P53_2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_P53_1.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_NEG_2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_P53_3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/NEG2_peptides_1_1_0.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/P53-1_peptides_1_1_0.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/NEG3_peptides_1_1_0.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/P53-3_peptides_1_1_0.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/P53-2_peptides_1_1_0.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/NEG1_peptides_1_1_0.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_NEG_3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_P53_1.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_P53_2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_NEG_1.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_P53_3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075858/19-JAN-26_SB-IP_NEG_2.mgfprimaryOK200miguel.de-lucas@durham.ac.ukMiguel de LucasData-dependent acquisitionAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryBottom-up proteomicsNot availableArabidopsisP53https://www.ebi.ac.uk/pride/archive/projects/PXD075858RootTransgenic XVE: p53 seeds were germinated in liquid Gamborg B5 medium supplemented with B5 vitamins and sucrose and grown under constant agitation for three weeks in the dark to promote root growth. To induce p53 expression, β-estradiol was added to the growth medium at a final concentration of 10 μM 24 hours prior to harvesting; an equivalent volume of DMSO was added to control samples. Harvested tissue was blotted dry, immediately snap-frozen in liquid nitrogen, and stored at −80°C until further processing. For protein extraction, frozen tissue was ground to a fine powder using a pre-chilled mortar and pestle and resuspended in extraction buffer containing 50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 0.5% Triton X-100, 1 mM PMSF, and a protease inhibitor cocktail. Crude extracts were clarified by centrifugation, and the resulting supernatant was used as input for immunoprecipitation (IP). For the IP, Dynabeads sheep anti-mouse IgG were washed 3 x in extraction buffer without the triton and PMSF and then pre-coupled tumbling for 1 h at 4ºC with anti-p53 DO-1 (2 µg per IP, Santa Cruz). Lysates were added to the beads and incubated overnight at 4ºC. After this the beads were washed with ammonium bicarbonate (ABC) to remove detergent and unspecific binders. The proteins were then reduced by 100 mM DTT for 30 min, followed by alkylating with iodoacetamide for 30 min in the dark. The samples were trypsinised (Promega) at 37ºC overnight at 700 rpm. The beads were washed with acetonitrile (ACN). After the peptides were eluted with 2% DMSO and ACN. This was diluted with 0.1% formic acid (FA) until the DMSO concentration reached <1%, this was loaded on the mass spectrometer.PrideNot availableIP-digest eluates were dried, and the residue resuspended in 0.5% formic acid (FA) for desalting using C18 Stage tips. Resulting peptide residues were resuspended in 0.1% FA for top-30 data-dependent LC-MS-MS analysis on a TripleTOF 6600 mass spectrometer linked to an Eksigent 425 LC via a DuoSpray 2 source (Sciex). Sample injection and peptide separation was in trap and elute mode using YMC-TriArt C18 columns (trap, part no. TA12S05-E5J0RU, resolving TA12S03-15H0RU) at a flow rate of 0.5 µL/min. Buffer A was 0.1% FA in water and B 0.1% FA in acetonitrile and peptides eluted in sequential gradients of: 3 - 8% B over 3 minutes, 8 – 30% B over 35’, 30-40 % B over 9 minutes, followed by a 2 minute ramp to 80 % B and a column wash for 5 minutes before re-equilibration in 3% buffer B. MS data acquisition was for 50.5 minutes after valve switching to bring the trap in-line and the mass spectrometer cycle time of 1.2 seconds comprised a 0.25 sec precursor MS1 scan (350 – 1600 m/z) followed by 30 MS-MS acquisitions of 30 msec (100 – 1500 m/z range). MS-MS was triggered by precursors of +2 to +5 charge with >500 cps intensity and a rolling exclusion of 15 seconds was applied throughout to limit selection of the same precursor multiple times. Datafiles in wiff format were processed using PEAKS X-Pro (Bioinformatics Solutions Inc) using a database containing the Arabidopsis thaliana proteome, known proteomic experiment contaminants and the human p53 protein sequence, a total of 33,781 entries. Amino acid modifications were fixed carbamidomethyl [C] and variable oxidised methionine. Post-processing, the peptide FDR was set to 1% against a reversed decoy database, the peptide de novo ALC set to >80%, protein FDR set to 1% and a filter of 2 unique peptides per protein was applied. Identified protein and protein-peptide lists were exported from PEAKS for further analysis.ProteomicsMiguel de LucasCOMPLETEDurham UniversityArabidopsis Thaliana (mouse-ear Cress)Not availablemiguel.de-lucas@durham.ac.ukDurham universityUnited Kingdom10.6019/PXD075858falseA versatile inducible plant model system for dissecting p53 function and discovering novel interaction networksWith the aim of revealing potential conserved or novel regulatory partners that could explain the phenotypes present on plant cells expressing p53, we performed p53-immunoprecipitation in combination with mass spectrometry (IP-MS) on 3-week-old XVE:p53 root cultures treated with DMSO (control) or 10µM ß-estradiol (inducer) for 24h.2026-06-202026-03-19PXD075858NEWT:6945NEWT:184922NEWT:6703NEWT:3555NEWT:71647NEWT:2NEWT:157546NEWT:474186NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:1496NEWT:544496NEWT:2102NEWT:2042546NEWT:259447NEWT:45351NEWT:445974NEWT:43179NEWT:4513NEWT:180454NEWT:5722NEWT:1247NEWT:6938NEWT:1129NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:281395NEWT:10360NEWT:1211601NEWT:876138NEWT:47664NEWT:317548NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:272563NEWT:1147161NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:82688NEWT:95648NEWT:3885NEWT:3888NEWT:5821NEWT:1589NEWT:44139NEWT:135622NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559NEWT:28909NEWT:515849NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:913645NEWT:1000589NEWT:85963NEWT:85962NEWT:143361NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4442NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NEWT:2164133NCBITaxon:183674NEWT:1316931NEWT:224308NEWT:167387NEWT:84645NEWT:44586NEWT:626528NEWT:3347NEWT:511145NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:211586NEWT:747078NEWT:1282NEWT:1283NEWT:431241NEWT:931281NEWT:4550NEWT:1000561NEWT:2133NEWT:294381NEWT:197NEWT:1390363NEWT:77133NEWT:288705NEWT:29176NEWT:145481NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:556182NEWT:1270NEWT:374990NEWT:1392NEWT:498217NEWT:156471NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:156476NEWT:286NEWT:391619NEWT:360104NEWT:246196NEWT:287NEWT:246197NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:161934NEWT:1148NEWT:580240NEWT:5508NEWT:294128NEWT:5507NEWT:11676NEWT:55571NEWT:35500NEWT:1140NEWT:100226NEWT:4530NEWT:1143NEWT:4896NEWT:75058NEWT:13616NEWT:1390NEWT:1094343NEWT:1336795NEWT:644042NEWT:296543NEWT:316435NEWT:42157NEWT:1773NEWT:1895NEWT:1182590NEWT:3712NEWT:82380NEWT:1034304NEWT:105023NEWT:866628NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:375146NEWT:9378NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NEWT:8175NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:47946NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:1077286NEWT:943129NEWT:243277NEWT:990119NEWT:7067NEWT:2850NEWT:1111708NEWT:408172NEWT:227321NEWT:408170NEWT:493760NEWT:106590NEWT:260710NEWT:257313NEWT:3827NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:930945NEWT:106592NEWT:536231NEWT:46704NEWT:1436733NEWT:460519NEWT:1187947NEWT:572307NEWT:1432138NEWT:269796NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:1194599NEWT:272844NEWT:54571NEWT:9598NEWT:8030NEWT:9483NEWT:1513458NCBITaxon:40559NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:759272NEWT:432359NEWT:46835NEWT:1182263NEWT:109757NEWT:943146NEWT:2711NEWT:300852NEWT:537457NEWT:1502NEWT:376686NEWT:95486NEWT:9103NEWT:508771NEWT:1883446NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:29158NEWT:644223NEWT:3635NEWT:5811NEWT:235443NEWT:180923NEWT:108458NEWT:272623NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:118499NEWT:169963NEWT:32644NEWT:527796NEWT:225117NEWT:746128NEWT:499175NEWT:109779NEWT:43665NEWT:1266464NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:367830NEWT:1255228NEWT:178616NEWT:649908NEWT:410289NEWT:373153NEWT:375451NEWT:352472NEWT:357NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:411469NEWT:84023NEWT:1679NEWT:559292NEWT:39491NCBITaxon:5811NEWT:29491NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:1328426NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NCBITaxon:138NEWT:40483NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:38293NEWT:1428NEWT:327159NEWT:178876NEWT:1660NEWT:327160NEWT:573NEWT:9031NEWT:1872122NEWT:7091NEWT:108931NEWT:241368NEWT:1055524NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:7237NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:187878NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1821314NEWT:1249668NEWT:7108NEWT:40479NEWT:317NEWT:5286NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:9644NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:273068NEWT:554NEWT:27592NEWT:98334NEWT:426428NEWT:451516NEWT:63459NEWT:1276815NEWT:36185NEWT:588858NEWT:1225786NEWT:9639NCBITaxon:11071NEWT:242231NEWT:7574NEWT:1715256NEWT:197221NEWT:7215NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:2172103NEWT:6494NEWT:7460NEWT:6491NEWT:507601NEWT:434271NEWT:643680NCBITaxon:6157NEWT:42752NEWT:746360NEWT:6239NEWT:89764NEWT:470150NEWT:162425NEWT:216257NEWT:102169NEWT:543734NEWT:9986NEWT:4054NEWT:73239NEWT:38018NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:118503NEWT:2059687NEWT:115357NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NEWT:13164NEWT:216129NCBITaxon:2NEWT:985076NEWT:1215323NEWT:2664179NEWT: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