Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK15.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK19.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK18.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK16.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK20.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK17.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/ACE_0869_NK12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/UP000005640_9606_OPPG.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/Sample_Legend_and_LC-MS_Settings_v01.docxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063889/Search.zipprimaryOK200farnusch.kaschani@uni-due.deFarnusch KaschaniData-dependent acquisitionMass SpectrometryLc-msPull-downUsp7https://www.ebi.ac.uk/pride/archive/projects/PXD063889Pull-down samples were washed on bead and then taken up in Lysis buffer (final concentrations; 1% SDS, 10 mM TCEP, 40 mM Chloracetamide, 50 mM HEPES). Beads were boiled 90°C 5 min and cleared. Supernatant was transferred to fresh tube (~50 µL Volume). Then, 3 µL of a 50 µg/µL 1:1 mixture of hydrophilic (#45152105050250) and hydrophobic (#65152105050250) carboxylate modified Sera-Mag SpeedBeads (Cytiva), that were washed twice with MS-grade water, were added to the samples. The next steps were carried out at room temperature unless noted otherwise. Afterwards, the samples were mixed shortly (1 min, 1000 rpm) and collected by short centrifugation (10 s, 200 ×g). Protein binding was induced by the addition of an equal volume of pure ethanol (10 min, 1000 rpm), the beads were collected by a brief centrifugation step (10 sec, 200 ×g) and the plate was placed on a magnetic stand. Beads were allowed to bind for at least 5 min before the supernatant was removed. The beads were then taken up in 180 µL 80% ethanol and transferred to a fresh multiwell plate. Subsequently the beads were washed four times with 180 µL 80% (v/v) ethanol prior to the addition of 100 µL digestion enzyme mix (0.6 μg of trypsin (V5111; Promega) and 0.6 µg LysC (125-05061; FUJIFILM Wako Pure Chemical) in 25 mM ammonium bicarbonate). Samples were incubated at 37 °C for 19 h while shaking (1300 rpm). On the next day, the samples were briefly centrifuged (10 s, 200 ×g) and placed on a magnet for 5 min. The clear solution containing the tryptic peptides was transferred to a fresh multiwell plate. The beads were taken up in 47 µL 25 mM ammonium bicarbonate and incubated while shaking (10 min, 1000 rpm). The plate was then placed on a magnetic stand and after 5 min the cleared supernatant was collected and combined with the recovered first peptide mix, followed by the addition of formic acid (FA) to a final concentration of 2% (v/v) for trypsin inactivation. Samples were then desalted on StageTips (Rappsilber et. al. 2007).PrideRAW spectra were submitted to an Andromeda (Cox et al. 2011) search in MaxQuant (2.5.2.0) using the default settings (Cox & Mann 2008). Label-free quantification and match-between-runs was activated (Cox et al. 2014 ). The MS/MS spectra data were searched against the Uniprot H. sapiens reference proteome (UP000005640_9606_OPPG; one protein per gene; 20606 entries, downloaded July 2023). All searches included a contaminants database search (as implemented in MaxQuant, 245 entries). The contaminants database contains known MS contaminants and was included to estimate the level of contamination. Andromeda searches allowed oxidation of methionine residues (16 Da) and acetylation of the protein N-terminus (42 Da). Carbamidomethylation on Cystein (57) was selected as static modification. Enzyme specificity was set to “Trypsin/P”. The instrument type in Andromeda searches was set to Orbitrap and the precursor mass tolerance was set to ±20 ppm (first search) and ±4.5 ppm (main search). The MS/MS match tolerance was set to ±0.5 Da. The peptide spectrum match FDR and the protein FDR were set to 0.01 (based on target-decoy approach). For protein quantification unique and razor peptides were allowed. Modified peptides were allowed for quantification. The minimum score for modified peptides was 40. Label-free protein quantification was switched on, and unique and razor peptides were considered for quantification with a minimum ratio count of 2. Retention times were recalibrated based on the built-in nonlinear time-rescaling algorithm. MS/MS identifications were transferred between LC-MS/MS runs with the “match between runs” option in which the maximal match time window was set to 0.7 min and the alignment time window set to 20 min. The quantification is based on the “value at maximum” of the extracted ion current. At least two quantitation events were required for a quantifiable protein. Further analysis and filtering of the results was done in Perseus v1.6.10.0. (Tyanova et al. 2016). Comparison of protein group quantities (relative quantification) between different MS runs is based solely on the LFQ’s as calculated by MaxQuant, MaxLFQ algorithm (Cox et al. 2014).ProteomicsFarnusch KaschaniPARTIALAnalytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, GermanyHomo Sapiens (human)Not availablefarnusch.kaschani@uni-due.deUniversity Duisburg-EssenGermanyfalseCompetitive target ID for inhibitor NK192Competitive target ID for inhibitor NK192. To this end the inhibitor was decorated with biotin and used in a pull-down experiment to pull out the desired on-target (USP7) and possible off-targets. The samples were analysed by LC-MS.2026-04-212025-05-13PXD063889NEWT: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:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:82688NEWT:95648NEWT:3885NEWT:3888NEWT:5821NEWT:1589NEWT: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: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: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:1513458NCBITaxon:40559NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:759272NEWT:432359NEWT:46835NEWT:1182263NEWT:109757NEWT:943146NEWT:2711NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:9103NEWT:508771NEWT:1883446NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:29158NEWT:3635NEWT:5811NEWT:235443NEWT:180923NEWT:108458NEWT:272623NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:118499NEWT:169963NEWT:32644NEWT:527796NEWT:225117NEWT:746128NEWT:499175NEWT:109779NEWT:43665NEWT:1266464NEWT:1715989NEWT:476272NEWT:3747NEWT:195051NEWT: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:36185NEWT:588858NEWT:1225786NEWT:9639NCBITaxon:11071NEWT:242231NEWT:7574NEWT:1715256NEWT:197221NEWT:7215NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:2172103NEWT:6494NEWT:7460NEWT:6491NEWT:507601NEWT: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:986NEWT:52641NEWT:7038NEWT:7159NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:27448NEWT:366581NEWT:216599NE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