Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/combined_peptide.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/combined_protein.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/Experimental_conditions.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP_B_S3-F4_1_5297.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP2_PP_A_S3-F3_1_5296.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP2_PP_B_S3-F6_1_5299.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP2_A_S3-F2_1_5295.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP2_PP_C_S3-F9_1_5302.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP2_C_S3-F8_1_5301.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP_D_S3-F10_1_5303.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP2_D_S3-F11_1_5304.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP_C_S3-F7_1_5300.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/fragger.paramsftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP2_B_S3-F5_1_5298.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP2_PP_D_S3-F12_1_5305.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD063432/AD_MS_043_PP_A_S3-F1_1_5294.d.zipprimaryOK200a.barnard@imperial.ac.ukAmrita DateData-dependent acquisitionMass SpectrometryBottom-up proteomicsPyrrolopyrimidineAffinity-based protein profilingΑ-helix mimeticsMdm2https://www.ebi.ac.uk/pride/archive/projects/PXD063432SJSA-1 cells were treated with helix mimetic parent/ helix mimetic probes/helix mimetic probe + parent (2 x concentration)for 4 h in serum-free media. Cells were then irradiated at 365 nm for 2 min, and lysed with 1% SDS. CuAAC was carried out with azide-PEG3-biotin. Protein was precipitated using chloroform and methanol and the pellet was washed (x2) with methanol. Protein pellet was resuspended in 0.2% SDS in 50 mM HEPES buffer, pH 8.0. Labelled proteins were enriched on Neutravidin agarose resin for 2 h at rt. Supernatant was removed and resin was washed. Resin was resuspended in 0.2% SDS in HEPES buffer, and reduction and alkylation was carried out using TCEP (10 mM) and 2-chloroacetamide (40 mM). After 10 min, supernatant was removed and resin was washed with buffer (x2), before resuspending in 50 mM HEPES pH 8.0. 0.2 ug trypsin was added, and samples were digested overnight at 37 degrees. Supernatant was collected and loaded onto Evotips for processing using nanoLC-MS/MS using an Evosep One coupled with a timsTOF HT (Bruker) equipped with an 8 cm × 150 µm, 1.5 µm analytical column (Evosep).PrideddaPASEF Bruker .d files were processed using Fragpipe version 20.0 (Nesvilab).10 Data was searched against a human reference proteome with isoforms (Uniprot, UP000005640, accessed 6 June 2022, 203368 proteins) with 50% decoys and contaminants added. The built-in label-free quantification-match between runs workflow was used. Bruker .d files were searched using MSFragger (version 3.8) The following parameters were used: strict trypsin digestion; a maximum of 2 missed cleavages allowed; precursor ion tolerance of 20 ppm; trimming of protein N-terminal methionine; oxidation (M) and N terminal acetylation as variable modifications; carbamidomethylation (C) as a fixed modification. MaxLFQ minimum ions was set to 1 and the retention time tolerance for match between runs was set to 2 min. All other default parameters were used for processing. MSFragger search results were processed using Percolator (version 3.5) for peptide-spectrum match validation, followed by Philosopher (version 5.0.0) for protein and FDR filtering. Label-free quantification values were calculated using the MaxLFQ algorithm using IonQuant (version 1.9.8) with match between runs enabled and min ions set as 1.ProteomicsAnna BarnardImperial College LondonPARTIALHomo Sapiens (human)a.date19@imperial.ac.uk10.1039/D6CB00065GImperial College LondonUnited KingdomfalseAfBPP of pyrrolopyrimidine α-helix mimeticsA wide range of small molecule scaffolds capable of mimicking protein α-helices to modulate protein-protein interactions have been reported, yet their target selectivity is poorly understood. Here, we report the affinity-based protein profiling of three structurally distinct classes of α-helix mimetics, N-substituted oligobenzamides, pyrrolopyrimidines, and oxopiperazines, all reported to inhibit the interaction between the tumour suppressor protein p53 and its negative regulator murine double minute 2 (MDM2).2026-08-052025-04-29PXD063432NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:9778NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:2042546NEWT:115104NEWT:1081927NEWT:67825NEWT:43179NEWT:13076NEWT:1249668NEWT:376741NEWT:317NEWT:55153NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:415540NEWT:876138NEWT:4081NEWT:554NEWT:98334NEWT:426428NEWT:237561NEWT:6928NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:3885NEWT:746360NEWT:6239NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:3641NEWT:8782NEWT:1263854NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:1283NEWT:931281NEWT:1000561NEWT:7029NEWT:1283300NEWT:6183NEWT:334747NEWT:61235NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:185431NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:7370NEWT:75058NEWT:83906NEWT:607699NEWT:6282NEWT:208964NEWT:1134506NEWT:575584NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:6669NEWT:10090NEWT:935293NEWT:64152NEWT:749200NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:100816NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:5689NEWT:645463NEWT:544404NEWT:3702NEWT:129249NEWT:9925NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:128161NEWT:106592NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:1424507NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:10306NEWT:1911079NEWT:8022NEWT:145943NCBITaxon:4932NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:59202NEWT:9975NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:1147787NEWT:72407NEWT:9606NEWT:367830NEWT:157295NEWT:178616NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:360094NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:33952NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:9940NEWT:327160NEWT:573NEWT:9031NEWT:1274420NEWT:70910009-0008-4891-1643