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Henry"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"software":[""],"submitter_keywords":["Tunicamycin","Lc-ms/ms","Cho","Stress"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD069782"],"tissue":["Permanent Cell Line Cell"],"sample_protocol":["Peptide samples were resuspended in 50 μL with LC-LOAD buffer and 2 μL from each sample were analysed using an UltiMate 3000 nanoRSLC system (Thermo Scientific, UK) interfaced with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific, UK). Peptides were loaded onto a C18 trapping column (Acclaim PepMap100, 300 μm × 5 mm, Thermo Scientific) at a flow rate of 25 μL/min using 2% (v/v) acetonitrile (ACN) and 0.1% (v/v) trifluoroacetic acid (TFA) for 3 min for desalting and concentration. Separation was performed on an analytical column (Acclaim PepMap100, 75 μm × 50 cm, 3 μm particle size, Thermo Scientific) using a binary gradient of solvent A (0.1% formic acid in LC-MS grade water) and solvent B (80% ACN, 0.08% formic acid in LC-MS grade water). The gradient consisted of 2–27.5% solvent B over 100 min, 27.5–90% over 10 min, followed by a 5 min hold at 90% B, at a flow rate of 300 nL/min. Peptides were ionised using nano-electrospray ionisation at 2.0 kV and 320 °C. Full MS scans were acquired in the Orbitrap at a resolution of 120,000 (at m/z 200), with an automatic gain control (AGC) target of 4 × 10⁵ and a maximum injection time of 50 ms. Data-dependent acquisition was employed with a scan range of 380–1500 m/z and a top- speed MS/MS acquisition algorithm. Precursor ions were selected with charge states from 2+ to 7+ and dynamically excluded for 60 s after initial selection. Fragmentation was performed using higher-energy collisional dissociation (HCD) with a collision energy of 28%. MS/MS spectra were acquired in the linear ion trap with an AGC target of 2 × 10⁵ and a maximum injection time of 32 ms."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Peptide identification was performed using Proteome Discoverer 2.2 (Thermo Scientific, UK) with the SEQUEST HT algorithm against a Cricetulus griseus UniProt database (downloaded May 2023). Search parameters included a precursor mass tolerance of 10 ppm and fragment mass tolerance of 0.6 Da. Carbamidomethylation of cysteine was set as a static modification, and oxidation of methionine was set as a dynamic modification. Trypsin was selected as the digestion enzyme, allowing up to two missed cleavages. Peptide- spectrum matches were filtered at a false discovery rate (FDR) of <1% using Percolator. Label-free quantitative analysis was performed using Progenesis QI for Proteomics (NonLinear Dynamics, Waters, UK). Peptides with charge states of +2, +3, and +4 were considered, and normalised abundances were used for statistical analysis. Peptides with a one-way ANOVA p-value ≤ 0.05 between treatment groups were exported for protein identification. Proteins were considered differentially expressed if they met the following criteria: (i) ANOVA p-value ≤ 0.05, (ii) at least two unique peptides, and (iii) a fold change ≥ ±1.5 between the experimental groups."],"omics_type":["Proteomics"],"labhead":["Dr. Paula Meleady"],"instrument_platform":[""],"labhead_affiliation":["School of Biotechnology, Dublin City University, Dublin, Ireland"],"submission_type":["COMPLETE"],"species":["Cricetulus Griseus (chinese Hamster) (cricetulus Barabensis Griseus)"],"submitter_mail":["michael.henry@dcu.ie"],"publication":["41750347 Sideri CK, Ryan D, Henry M, Efeoglu E, Meleady P. Proteasome Inhibition Amplifies Endoplasmic Reticulum (ER) Stress Responses: Comparative Proteomics of Chinese Hamster Ovary Cell Lines. Biomolecules. 2026 16(2):277 10.3390/biom16020277"],"submitter_affiliation":["NICB - DCU"],"submitter_country":["Ireland"],"doi":["10.6019/PXD069782"],"pubmed_abstract":["Chinese hamster ovary (CHO) cells are widely utilised in the biopharmaceutical industry to produce therapeutic proteins. Understanding the mechanisms of endoplasmic reticulum (ER) stress and its interplay with protein degradation pathways remains pivotal for improving production efficiency and product quality. In this study, we investigated the proteomic responses of CHO-K1 (non-producer), CHO DP-12 (IgG-producer), and NISTCHO (IgG-producer) cell lines under ER stress induced by a combination of the proteasome inhibitor MG132 and the glycosylation inhibitor tunicamycin. Viability, cell growth, and IgG titre were measured after 24 h, 48 h, and 72 h of treatment and the 48 h timepoint was used for the comparative analysis of the proteomic data across the three cell lines. Proteasome inhibition with MG132 intensified ER stress and altered ER-associated protein degradation (ERAD). Combined tunicamycin + MG132 treatment was associated with cell line-specific proteomic changes: NISTCHO upregulated ER translocation and glycoprotein quality control proteins (SSR4, SEC24C, UGGT1), CHO DP-12 activated redox/disulfide regulators (DNAJC10, CAPN1), while CHO-K1 showed broad proteome shifts, suggesting differences in baseline stress handling. These findings provide mechanistic insights into ER stress and protein quality control in CHO cells, offering a foundation for strategies to enhance cell line robustness and optimise biopharmaceutical production."],"pubmed_title":["Proteasome Inhibition Amplifies Endoplasmic Reticulum (ER) Stress Responses: Comparative Proteomics of Chinese Hamster Ovary Cell Lines."],"pubmed_authors":["Sideri Christiana-Kondylo CK, Ryan David D, Henry Michael M, Efeoglu Esen E, Meleady Paula P"],"additional_accession":[]},"is_claimable":false,"name":"Comparative label-free proteomic analysis of multiple CHO cell lines under tunicamycin-induced ER stress and proteasome inhibition","description":"Chinese Hamster Ovary (CHO) cells are widely utilised in the biopharmaceutical industry to produce therapeutic proteins. Understanding the mechanisms of endoplasmic reticulum (ER) stress and its interplay with protein degradation pathways remains pivotal for improving production efficiency and product quality. Proteasome inhibitors such as MG132 offer a valuable tool for studying ER stress by disrupting protein degradation and promoting the accumulation of ubiquitinated proteins. In this study, we investigated the proteomic responses of CHO-K1 (non-producer), CHO DP-12 and NISTCHO (IgG producer) cell lines under ER stress induced by a combination of the proteasome inhibitor MG132 and the glycosylation inhibitor tunicamycin. The combined treatment of MG132 and tunicamycin intensified ER stress by preventing the degradation of ubiquitinated misfolded proteins, activating the unfolded protein response (UPR) more robustly than either agent alone. Key pathways related to protein folding, ER- associated degradation (ERAD), and the ubiquitin-proteasome system were significantly altered, particularly in the producer cell line NISTCHO. By modulating stress responses and protein degradation pathways, this work contributes to improving the yield and quality  of biopharmaceuticals in industrial production settings.","dates":{"publication":"2026-08-17","submission":"2025-10-22"},"accession":"PXD069782","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:475174","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:491","NEWT:460523","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:227377","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:105487","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:7375","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:2925","NEWT:214053","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:29829","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:48106","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:90690","NEWT:1436183","NEWT:300273","NEWT:4232","NEWT:416348","NEWT:11298","NEWT:4236"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