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Following treatment, cells were harvested, washed twice with PBS, and pellets were flash frozen in liquid nitrogen before being stored at -80 °C. Samples were prepared using the single-pot, solid-phase-enhanced sample-preparation (SP3) strategy.1 All buffers and solutions were prepared with mass spectrometry (MS)-grade water (Avantor). Cell pellets were taken up in 100 µL 1x sample buffer (50 mM Hepes pH 8.0, 1% (wt/v) SDS, 1% (v/v) NP-40, 10 mM TCEP, 40 mM chloroacetamide) and samples were heated at 90°C for 5 min prior to sonication with a Bioruptor UCD-300 (Diagenode) for ten cycles of 1 min pulse and 30 s pause at high power. The samples were then supplemented with Benzonase (20 U/sample) and sonified for 5 min in a water bath (Bandelin) followed by 30 min incubation at 30 min. Next the protein extracts were centrifuged (20000 xg, RT, 40 min) and the protein concentration of the cleared lysates was determined using the Pierce 660 nm Protein Assay Reagent (#22660; Thermo Scientific) with the Ionic Detergent Compatibility Reagent (#22663; Thermo Scientific) according to the manufacturers’ instructions. Next, 15 µg of total protein per sample in a volume of 100 µL sample buffer was transferred to a 500 µL 96-well plate and treated with 7 U of benzonase (#71206; Merck Millipore) in dilution buffer (20 mM Hepes pH 8.0, 2 mM MgCl2) at 37 °C for 30 min with gentle agitation at 1500 rpm. After Benzonase treatment samples were heated to 90°C for 5 min and after cooling down to room temperature, iodoacetamide to a final concentration of 10 mM was added for complete alkylation of cysteines (37 °C, 15 min, 1000 rpm, in the dark). 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). LC-MS/MS Analysis: LC-MS/MS analysis of peptide samples was performed on an Orbitrap Fusion Lumos mass spectrometer (Thermo Scientific) coupled to a Vanquish Neo ultra high-performance liquid chromatography (UHPLC) system (Thermo Scientific) that was operated in the one-column mode. Detailed information about the LC-MS settings can be found in file Sample_Legend_and_LC-MS_Settings_v01.docx (part of this submission)."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["RAW 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)."],"omics_type":["Proteomics"],"labhead":["Farnusch Kaschani"],"instrument_platform":[""],"labhead_affiliation":["Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["farnusch.kaschani@uni-due.de"],"submitter_affiliation":["University Duisburg-Essen"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Pancreatic cancer cell samples (DDA)","description":"Whole proteome measurement to determine selectivitiy profile for compound NK250 in pancreatic cancer as well as determining downstream signaling effects of DUB inhibition and degradation.","dates":{"publication":"2026-04-21","submission":"2025-05-14"},"accession":"PXD063913","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:1247","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:5821","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:28909","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:747078","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NEWT:1390363","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:498217","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:391619","NEWT:360104","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:105023","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:269796","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:1182263","NEWT:109757","NEWT:943146","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:118499","NEWT:169963","NEWT:32644","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:7237","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:9644","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:27592","NEWT:98334","NEWT:426428","NEWT:588858","NEWT:9639","NCBITaxon:11071","NEWT:242231","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:2172103","NEWT:6494","NEWT:7460","NEWT:6491","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:42752","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:543734","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:118503","NEWT:435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