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Cell culture media from 5 min CAP irradiated A549 cells were transferred to un-irradiated (bystander) A549 cells 1 h post-irradiation. Proteins were extracted from sham-irradiated controls, direct CAP-exposed and bystander cells after 4 h incubation at 37 ◦C in a humidified, 5% CO2 atmosphere. Three experimental replicates were used for the study. Proteins were extracted from the samples using sonication in 0.5 M triethylammonium bicarbonate (TEAB) buffer containing 1x protease inhibitor cocktail (Roche Diagnostics, GmbH, Germany). The sample extract was centrifuged at 20,000 × g for 40 min at 4oC and the clear supernatant containing proteins was collected. The protein concentration was determined by bicinchoninic Acid (BCA) method.  Protein samples (50 μg) were reduced in presence of 20 mM dithiothreitol (DTT) at 60°C for 60 min and alkylated in 40 mM iodoacetamide (IAA) for 30 min in the dark at room temperature. Sequencing grade trypsin (Thermo Fisher Scientific, Waltham, MA, USA) was added at a protein-to-trypsin ratio of 30:1 and digestion was performed over night at 37 °C. The extracted peptides from each sample were purified using Pierce C18 spin columns. The extracted tryptic peptides were analysed by using Q-Exactive Plus tandem mass spectrometer connected to an EASY-nLC 1200 instrument (Thermo Fisher Scientific, Waltham, MA, USA). The positive ionization mode was employed for operating the mass spectrometer using a data-dependent acquisition (DDA) approach. The MS1 spectra were acquired in the m/z range of 350−2000 m/z under 70,000 resolutions with an AGC target of 1E6 and maximum injection time of 60 ms. A lock mass of 445.12003 Da was used as internal standard for mass calibration. The MS2 fragmentation was carried out on the Top 15 precursors with the highest abundance. The charge exclusion criteria included unassigned ions, 1+ ions, and ions with a charge greater than 7+. High-energy collision dissociation (HCD) was utilized for the fragmentation process employing normalized collision energy of 27 eV. The MS2 spectra were acquired using an Orbitrap mass spectrometer within the scan range of 200 to 2000 m/z at a resolution of 17,500. The instrument operated with an AGC target of 2E5 and a dynamic exclusion window of 35 s. The maximum injection time allowed for each scan was set to 120 ms. The MS experiments were performed in biological triplicates."],"repository":["Pride"],"labhead":["Anu Ghosh"],"instrument_platform":[""],"submission_type":["COMPLETE"],"labhead_affiliation":["AHF&RSS, Radiation Biology & Health Sciences Division, Bio-Sciences Group, Bhabha Atomic Research Centre, Mumbai 400 085, India."],"publication":["42414516 Ghosh S, Nishad S, Vaid A, Baijal NN, Visani A, Rane R, Joseph A, Ghosh A. Non-canonical ATR signaling mediates direct and bystander cold atmospheric plasma-induced stress responses in A549 lung adenocarcinoma cells. Sci Rep. 2026 10.1038/s41598-026-60839-6"],"submitter_affiliation":["Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400 085, India"],"labhead_mail":["anugh@barc.gov.in"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"disease":["Lung Carcinoma"],"submitter_keywords":["Bhabha atomic research centre","And ghosh anu*","Bio-sciences group","Phd. radiation biology & health sciences division","Mumbai 400 085","Phd.","Proteomic analysis of cold atmospheric plasma induced bystander signalling in human lung carcinoma a549 cells.  s nishad","Ghosh somnath","Phd","India  *email: anugh@barc.gov.in"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD043888"],"quantification_method":[""],"modification":[""],"data_protocol":["The collected raw MS/MS data files from all samples were analysed using Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific, Waltham, MA, USA) software. SEQUEST search algorithm in the software was used to identify protein by searching against the Swiss-Prot Homo sapiens database (Tax id 9606, entries: 82,492). Precursor mass tolerance of 10ppm and a fragment tolerance 0.05 Da with maximum of two missed cleavage were allowed. Carbamidomethylation of Cysteine (+57.021 Da) was chosen as static modification. Methionine oxidation (+15.995 Da) and N-terminal acetylations (+42.011 Da) were set as dynamic modifications. FDR cut-off of ≤ 1% was set for peptide and protein identification using the target decoy database. Minimum of one unique peptide was included for identification of each confident protein. The label-free quantification (LFQ) algorithm of Proteome Discoverer 2.2.0.388 software was used for calculation of relative protein abundance in treatment replicate groups."],"omics_type":["Proteomics"],"species":["Homo Sapiens (human)"],"submitter_mail":["nishad@barc.gov.in"],"submitter_country":["India"],"doi":["10.6019/PXD043888"],"additional_accession":[]},"is_claimable":false,"name":"Proteomic analysis of cold atmospheric plasma induced bystander signalling in human lung carcinoma A549 cells.  S Nishad, PhD, Ghosh Somnath, PhD., and Ghosh Anu*, PhD. Radiation Biology & Health Sciences Division, Bio-Sciences Group, Bhabha Atomic Research Centre, Mumbai 400 085, India  *Email: anugh@barc.gov.in","description":"The radiation-induced bystander effect is defined by the presence of biological effects in cells that were not themselves in the field of irradiation. Plasma, as the fourth state of matter contains numerous active components including photons, free radicals, mild heat, electrons and ions. Cold atmospheric plasma (CAP) has been widely applied in biology and medicine including cancer treatments. However, contributions of CAP induced bystander effect have not been studied. Proteomic profiles obtained from direct CAP-exposed and un-irradiated (bystander) A549 cells were compared to understand enriched proteins or pathways altered under the bystander conditions.","dates":{"publication":"2026-07-09","submission":"2023-07-19"},"accession":"PXD043888","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:309807","NEWT:10245","NEWT:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:43186","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:661410","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:35786","NEWT:1580","NEWT:96731","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:641809","NEWT:27933","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:79329","NEWT:4442","NEWT:192875","NEWT:1214915","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:160621","NEWT:212790","NEWT:931281","NEWT:4432","NEWT:5762","NEWT:5763","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NEWT:2246","NEWT:2652724","NEWT:1912919","NEWT:5757","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:1367269","NEWT:145458","NEWT:633149","NEWT:10239","NEWT:68895","NEWT:44685","NEWT:161934","NEWT:4897","NEWT:1148","NEWT:5744","NEWT:5508","NEWT:3329","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1235816","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:2065263","NEWT:1772","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:52283","NEWT:11988","NEWT:284812","NEWT:8175","NEWT:400667","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:1246791","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:7070","NCBITaxon:287","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:9483","NEWT:333760","NEWT:56636","NEWT:1513458","NEWT:1233681","NCBITaxon:40559","NEWT:506599","NEWT:2853422","NEWT:81077","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:65349","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:109760","NEWT:943274","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:5936","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:1130798","NEWT:55529","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1116234","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:352472","NEWT:1071661","NEWT:1202532","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:1218097","NCBITaxon:50557","NEWT:39251","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:101841","NEWT:2014887","NEWT:33952","NEWT:153009","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:688333","NEWT:215402","NCBITaxon:548681","NEWT:318586","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:1308","NEWT:7091","NEWT:1034015","NEWT:760568","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:97477","NEWT:7111","NEWT:347515","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:8694","NEWT:4093","NEWT:4096","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:941442","NEWT:536088","NEWT:13076","NEWT:1226408","NEWT:7108","NEWT:40479","NEWT:43989","NEWT:4076","NEWT:142615","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:4084","NEWT:63577","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEW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