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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":["Data processing and analysis of DIA experiments (DIA-NN) Recorded RAW data was converted to the mzML file format using ProteoWizard (“peak Picking” (vendor MS level 1) as first filter, TPP compatibility, 64bit encoding precision, and index writing switched on) and analyzed with DIA-NN (version 1.8.1). DIA-NN was used in the library free mode. Spectral library generation is based on the Uniprot H. sapiens reference proteome (UP000005640_9606_OPPG; one protein per gene; 20606 entries, downloaded July 2023). For the search we selected “Trypsin/P” as protease with 2 missed cleavages allowed. As variable modifications we set “N-ter M excision”, “C carbamidomethylation”, “Ox(M)” and “Ac(N-term)”. The maximum number of variable modifications was set to 2. Peptide length was set from 7 – 30; Presursor charge range from 2 – 6. Precursor m/z range was set to 396 – 1004 and Fragment ion m/z range was set to 150 – 1800. Mass accuracy, MS1 accuracy and Scan window was kept at “0” (automatic). Unrelated runs, use isotopologues, MBR and no shared spectra were selected. Heuristic protein inference was based on “Genes”. Neural network classifier was set to “Single-pass mode”. Quantification strategy was set to “Robust LC (high precision) with cross-run normalization set to “RT & signal-dep.”. Library generation was set to “smart profiling” and Speed and RAM usage was set to “optimal results”. Precursor FDR was set to 1%.  For further data analysis and filtering of the DIA-NN output, the report.pg_matrix.tsv file which contains the normalized (MaxLFQ) protein group intensities was loaded into Perseus (v. 1.6.10.0). The data was transformed to the log2(x) scale and biological replicates were combined into categorical groups to allow comparison of the different treatment groups. For the full proteome analysis, only protein groups (PGs) with a valid LFQ intensity in at least two out of four replicates in a minimum of one categorical group were kept for further analysis. The log2-fold change in normalized protein group quantities between the different categorical groups was determined based on the mean LFQ intensities of replicate samples (relative quantification). To enable quantification, missing LFQ intensities were imputed from a normal distribution (width 0.3, down shift 1.8). The statistical significance of the difference in LFQ intensity was determined via a two-sided Student’s t-test."],"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 (DIA)","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 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