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LeeData-dependent acquisitionMass SpectrometryBottom-up proteomicsMultiple MyelomaQuantitative proteomicsPhosphoproteomicsMultiple myelomaProteasome inhibitor resistancehttps://www.ebi.ac.uk/pride/archive/projects/PXD077254B CellBone MarrowWild-type (WT) and matched bortezomib (BTZ)- and carfilzomib (CFZ)-resistant multiple myeloma cell lines (AMO-1, ARH77, L363, and RPMI8226) were cultured in independent biological triplicates. Cells were lysed in 40 mM Tris-HCl (pH 7.6) with 2% SDS, boiled at 95°C for 5 min, and treated with 1% TFA to hydrolyze DNA before quenching with 3 M Tris (pH 10) to a final pH of 7.8. Protein concentration was determined via BCA assay. Lysates were processed using an automated SP3 method on a Bravo liquid handling system. Proteins were reduced and alkylated on carboxylate beads in 50 mM HEPES (pH 8.5), 10 mM TCEP, and 50 mM CAA for 1 h at 37°C, followed by overnight digestion at 37°C using a 1:50 trypsin-to-protein ratio. Peptides were desalted and labeled with TMT 11-plex reagents. Four TMT batches were prepared, each containing triplicates of WT, BTZ-resistant, and CFZ-resistant lines from the same lineage, plus two bridge channels containing a pooled WT reference for cross-plex normalization. Pooled TMT-labeled peptides were fractionated via off-line basic reversed-phase (bRP) chromatography into 48 fractions. Approximately 15% of the fractionated peptides were reserved for global proteome LC-MS/MS analysis. The remaining fractions were pooled into 12 samples and subjected to Immobilized Metal Affinity Chromatography (IMAC) phosphopeptide enrichment using Fe(III)-NTA cartridges on an AssayMAP Bravo platform prior to LC-MS/MS acquisition.PrideNot availableRaw files were searched using MaxQuant (version 1.6.2.10) against the human UniProt reference database (downloaded November 30, 2020) supplemented with common contaminants. The experiment type was set to 11-plex TMT with reporter ion MS3 quantification. The false discovery rate (FDR) was set to 1% at both the peptide and protein levels. Cysteine carbamidomethylation was set as a fixed modification. Methionine oxidation and protein N-terminal acetylation were set as variable modifications. For the phosphoproteome dataset, phosphorylation of serine, threonine, and tyrosine (STY) was additionally included as a variable modification, and the "match between runs" feature was enabled (20 min alignment window, 0.7 min matching window). Default score cutoffs were applied, requiring a minimum Andromeda score of 40 and a delta score of 6 for modified peptides. Protein quantification was derived from summed peptide reporter intensities. For the phosphoproteome post-processing, the initial MaxQuant search results were further processed using SIMSI-Transfer (v0.5.0) with a p10 threshold to generate the final evidence files, and phosphosites were annotated using a custom Python package.ProteomicsBernhard KusterChair of Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, GermanyPARTIALHomo Sapiens (human)chienyun.lee@tum.de42362189 Lee CY, Han S, Haertle L, Munawar U, Vogt C, Streubel J, Besse A, Besse L, Driessen C, Einsele H, Waldschmidt J, Kortüm M, Kuster B. Proteome profiling reveals NQO2 activity contributing to proteasome inhibitor resistance in multiple myeloma cell lines. Mol Cell Proteomics. 2026:101615 10.1016/j.mcpro.2026.101615Chair of Proteomics and Bioanalytics, Technical University of Munich, GermanyGermanyProteasome inhibitors (PIs) are frontline therapies for multiple myeloma (MM). Although MM patients initially respond to PIs, resistance frequently emerges. While all PIs nominally target the same proteasomal catalytic subunit (PSMB5), the extent to which resistance mechanisms are the same or different among different PIs or between patients is poorly understood. To address this, we performed proteome and phosphoproteome profiling of 12 MM cell line models, comprising four parental lines (AMO-1, ARH77, L363, and RPMI8226) paired with lines that acquired resistance to bortezomib (BTZ) or carfilzomib (CFZ). Over 7000 proteins and up to 10,000 phosphopeptides were identified per cell line, enabling a comprehensive comparative analysis of shared and cell line-specific resistance signatures at the protein level. Data analysis revealed surprisingly few changes in the phosphoproteome but substantial reprogramming of the proteome in most models. Beyond known adaptations such as the overexpression of the PI target PSMB5 and the drug efflux transporter ABCB1, we identified the oxidoreductases NQO1 and NQO2 as significantly upregulated proteins under chronic proteotoxic stress across several models. Pharmacological follow up in PI resistant AMO-1 cells showed that NQO2 inhibition by imatinib fully restored CFZ sensitivity, validating NQO2 as a contributor to resistance formation in this model system.Proteome Profiling Reveals NQO2 Activity Contributing to Proteasome Inhibitor Resistance in Multiple Myeloma Cell Lines.Lee Chien-Yun CY, Han Seungbin S, Haertle Larissa L, Munawar Umair U, Vogt Cornelia C, Streubel Johanna J, Besse Andrej A, Besse Lenka L, Driessen Christoph C, Einsele Hermann H, Waldschmidt Johannes J, Kortüm Martin M, Kuster Bernhard BfalseDeep Proteomic and Phosphoproteomic Profiling in Proteasome Inhibitor-Resistant Multiple MyelomaProteasome inhibitors (PIs) are frontline therapies for multiple myeloma (MM). Although MM patients initially respond to PIs, resistance frequently emerges. While clinical PIs primarily target the same proteasomal catalytic subunit (PSMB5), the extent to which resistance mechanisms are shared among different PIs remains poorly understood. To elucidate these resistance mechanisms, we performed deep proteomic and phosphoproteomic profiling of 12 MM cell line models, comprising four parental lineages (AMO-1, ARH77, L363, and RPMI8226) and their paired derivatives with acquired resistance to bortezomib (BTZ) and carfilzomib (CFZ). We quantified over 7,000 proteins and up to 10,000 phosphopeptides per cell line, enabling a systematic comparative analysis of shared and cell line-specific resistance signatures. Crucially, we discovered that acquired PI resistance is primarily driven by massive, stable reprogramming of the global proteome, while the phosphoproteome remains surprisingly constrained. Alongside known adaptations such as the overexpression of the PI target PSMB5 and the drug efflux transporter ABCB1, we identified the antioxidant flavoenzymes NQO1 and NQO2 as significantly upregulated proteins under chronic proteotoxic stress. Importantly, our functional validation revealed that protein abundance does not strictly dictate essentiality; even in contexts with lower basal expression, NQO2 serves as a critical vulnerability. Co-inhibiting NQO1 alongside the established ABCB1 efflux pump effectively restored PI sensitivity. Collectively, our dataset provides a rich resource for MM research and reveals pan-NQO inhibition as a highly effective, actionable strategy to overcome PI resistance.2026-07-152026-04-16PXD077254NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:10245NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:43186NEWT:428146NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:1401257NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:1912919NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:1367269NEWT:145458NEWT:633149NEWT:1149786NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:1772NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:459758NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NEWT:272634NEWT:198107NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:552NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:377586NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:118562NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:9793NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:27457NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:419610NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:41307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