Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/PC9_MSstats_Output_PIVOT.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/A375_MSstats_Output_PIVOT.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/PC9_MSstats_annotation.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/A375_MSstats_annotation.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230731_AB_448.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230728_AB_427.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230727_AB_407.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230728_AB_419.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230727_AB_403.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230728_AB_415.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230728_AB_431.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230313_AB_145.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230313_AB_137.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230727_AB_387.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230728_AB_423.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230310_AB_104.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230727_AB_395.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230316_AB_166.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230731_AB_464.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230316_AB_162.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230310_AB_100.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230731_AB_456.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230316_AB_158.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230731_AB_452.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230316_AB_170.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230727_AB_399.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230728_AB_435.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230731_AB_460.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230316_AB_178.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230310_AB_092.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230310_AB_096.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230316_AB_174.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230310_AB_112.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230313_AB_129.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230313_AB_133.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230310_AB_108.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230727_AB_391.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230731_AB_468.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230313_AB_141.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/EXP480_230313_AB_125.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/PC9_txt.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063528/A375_txt.zipprimaryOK200s.surinova@ucl.ac.ukSilvia SurinovaData-dependent acquisitionMass SpectrometryBottom-up proteomicsHumanLc-ms/mshttps://www.ebi.ac.uk/pride/archive/projects/PXD063528Epithelial CellCell CultureFibroblastCells were lysed in 500 µL urea lysis buffer [50 mM triethylammonium bicarbonate, 8 M urea, cOmplete™, EDTA-free protease inhibitor cocktail (1:50 dilution) (Roche, 11873580001), 1 PhosSTOP tablet (Roche, 4906845001), 1 mM sodium orthovanadate] and lysates sonicated until clear. Protein concentration was measured using a BCA protein assay (Pierce #23227). 40 µg of protein was reduced with 5 mM tris(2-carboxyethyl)phosphine hydrochloride (Sigma C4706) at 37°C for 20 min and alkylated using 10 mM 2-chloroacetamide (Sigma 22790) for 20 min at room temperature in the dark. Peptides were digested with 400 ng LysC (FUJIFILM Wako 129-02541) for 4 h at 30°C, then diluted with 50 mM triethylammonium bicarbonate (Sigma T7408) to reduce the urea concentration down to 1.6 M. Samples were further digested with 800 ng Trypsin (Promega V5113) for 4 h at 37°C. Digest reactions were quenched by the addition of 10% trifluoroacetic acid (EMD Millipore 302031) to a final pH of 2. Sample desalting was performed using 7-70 µg C18 columns si(The Nest Group, Inc., HUM S18V) according to manufacturer’s specifications. Dried samples were stored at -80 °C and resuspended in 1% formic acid immediately prior to LC-MS/MS analysis.PrideRaw data were analysed with MaxQuant (version 2.2.0) where they were searched against the human SwissProt database (http://www.uniprot.org/, downloaded 27/07/2023) using default settings. Carbamidomethylation of cysteines was set as fixed modification, and oxidation of methionines and acetylation at protein N-termini were set as variable modifications. Enzyme specificity was set to trypsin with maximally 2 missed cleavages allowed. To ensure high confidence identifications, peptide-spectral matches, peptides, and proteins were filtered at a less than 1% false discovery rate (FDR). Label-free quantification in MaxQuant was used with a LFQ minimum ratio count of 2, Fast LFQ selected and the ‘skip normalisation’ option selected. The ‘match between runs’ feature was selected with a match time window of 0.7 min and an alignment time window of 20 min. For statistical analysis, the ‘proteinGroups.txt’ and ‘evidence.txt’ output files from MaxQuant were loaded into the MSstats statistical framework package (version 4.0) run through RStudio (version 1.3.1093, R version 4.0.3). Contaminants and reverse sequences were removed, data were log2 transformed, normalised by the global median, and a linear mixed-effects model was fitted to the data. The group comparison function was employed to test for differential abundance between conditions. p-values were adjusted to control the FDR using the Benjamini-Hochberg procedure.ProteomicsDr Silvia SurinovaPARTIALTeam Lead in Proteomics Head of the Proteomics Research Translational Technology Platform UCL Cancer Institute 72 Huntley Street, London, WC1E 6DD, UKHomo Sapiens (human)10.1016/J.IMMUNI.2026.02.005s.surinova@ucl.ac.ukUCLUnited KingdomfalseInduction of anti-tumour immunogenicity via modulation of nonsense-mediated decayThis project explores the role of SMG1 on the Nonsense-mediated decay (NMD) pathway in two human cell lines – PC9 (lung) and A375 (epithelial). The conditions used were a DMSO control for two SMG1 inhibitors, and an siRNA control for the siSMG1 RNA knock-down condition.2026-04-072025-05-01PXD063528NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:544496NEWT:5180NEWT:256737NEWT:115104NEWT:1081927NEWT:67825NEWT:13076NEWT:1249668NEWT:317NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:4081NEWT:876138NEWT:554NEWT:98334NEWT:237561NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:746360NEWT:6239NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:8782NEWT: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:931281NEWT:7029NEWT:1283300NEWT:334747NCBITaxon:79824NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:83332NEWT:29760NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:7370NEWT:6282NEWT:1134506NEWT:575584NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:10090NEWT:935293NEWT:749200NEWT:4120NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:373995NEWT:544404NEWT:3702NEWT:129249NEWT:8839NEWT:4232NEWT:990119NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:106592NEWT:9913NEWT:1432138NEWT:10312NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:10306NEWT:1911079NEWT:145943NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:9606NEWT:367830NEWT:157295NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:9940NEWT:573NEWT:9031NEWT:1274420NEWT:7091