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Arapidi"],"technology_type":["Immunopeptidomics","Data-dependent acquisition","Mass Spectrometry"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD077080"],"tissue":["Cell Culture"],"sample_protocol":["Cell lines used.The Jurkat (ATCC, TIB-152), K-562 (ATCC, CCL-243, USA) and HB-95 hybridoma cell lines (ATCC, HB-95) were used in the study. Jurkat and K-562 cell lines were cultured in RPMI 1640 medium (PanEco, C330p, Russia) 10% FBS (Gibco, 26140079, USA), 50 units/ml gentamicin (Dalhimfarm, Russia), 1.6 mM glutamine (GlutaMAX, Gibco, 35050061). All cell lines were cultured to the required number, then centrifuged for 5 min at 150 g (Eppendorf 5804 R, USA). The cell pellet was washed three times with Dulbecco's phosphate buffered saline, pH 7.4 (PanEco, P060). The supernatant was collected, and the cell pellet was stored at -80°C until further experiments. To produce antibodies to HLA I, HB-95 hybridoma cells (producer of HLA-ABC w6/32 antibodies, ATCC, HB-95) were cultured. Primary culture was performed in DMEM F12 Advanced medium (Gibco, 12634010) supplemented with 10% FBS (inactivation at 56°C for 30 minutes), 50 units/ml gentamicin, and 1.6 mM glutamine. When the cell density reached 600,000 cells/mL, the medium was replaced with one containing half as much FBS. This gradually reduced the FBS concentration in the medium. Once the FBS concentration reached 0.5%, the medium was replaced with HyClone ADCF-mab (Cytiva, SH30349.02, USA), 50 U/mL gentamicin, and 1.6 mM glutamine. Cells were cultured in this medium until 80-90% of the cells were killed, after which the supernatant containing antibodies was collected. Antibody concentrations in the cell medium were measured using the Easy-Titer mouse IgG Assay (Thermo Scientific, 23300, USA) according to the manufacturer's recommendations.All cells were regularly tested for mycoplasma contamination and cultured at 37°C and 5% CO2.Preparation of cell line lysates.When working with cell lines, 5 ml of lysis buffer (150 mM NaCl, 50 mM Tris-HCl, Protease Inhibitor Cocktail X100 (Thermo Scientific, 78438), and detergent) were added to the dried cell pellet and incubated for 1 hour on a multirotator (BioSan Multi-Bio RS-24) at 4°C. For lysis of the K-562 cell line, 1% NP-40 was used. Detergent concentrations were selected based on literature data, but were not less than twice the critical micelle concentration (CMC). The cell lysate was sonicated for 5 min (Elma S30H), then centrifuged for 15 min at 14,000 g and 4°C (Eppendorf 5804 R, rotor A-4-44), and the supernatant was collected.pHLA I Immunoprecipitation.For isolation, 1 ml of Pierce Protein A/G Agarose resin suspension (Thermo Fisher, 20422) was placed on a low-pressure chromatography column (Econo-Column 0.5x5 cm, Bio-Rad, USA). The resin was washed with 50 ml of phosphate-buffered saline (PBS, pH 7.4) at a flow rate of 1 ml/min. Cell medium obtained after culturing the HB-95 hybridoma was then loaded onto the column at a concentration of 2 mg of antibody per ml of resin. The cell medium was diluted 1:1 with PBS before loading. The column was washed with 5 ml of 150 mM NaCl and 50 mM Tris-HCl, after which the cell lysate was added and incubated for 2.5 hours using a peristaltic pump (Longerpump BT100-1L, Russia). The column was then washed sequentially with 50 ml of PBS, 5 ml of 150 mM NaCl, 50 mM Tris-HCl, and 10 ml of mQ, and eluted with 10 ml. pHLA I and antibody complexes were eluted with 10% acetic acid. After completion of the column run, it was washed with 50 ml of PBS and then preserved in PBS with 0.02% NaN3.The eluate was concentrated using a Concentrator plus centrifugal vacuum evaporator (Eppendorf, USA) at 60°C for 4.5 hours to 100–200 µl. The concentrated eluate was diluted with a solution of 3% acetonitrile in 0.1% TFA to 500 µl and sonicated for 5 minutes (Elma S30H ultrasonic bath). The peptides were then separated from the HLA complexes using centrifugal filtration cartridges (Vivaspin 500, 10 kDa) according to the manufacturer's protocol. The cartridges were additionally washed twice with 300 µl of 3% acetonitrile in 0.1% TFA. The peptides were dried in a Concentrator plus vacuum evaporator (Eppendorf) at 60°C for 6 hours and stored at -80°C until chromatograph mass spectrometry analysis.Chromatographic mass spectrometry analysis of HLA I ligands.Mass spectrometric analysis was performed on a Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher Scientific). The chromatographic system was assembled using a pre-column-column scheme (column: sorbent - Aeris Peptide XB-C18 (Agilent, USA), length - 15 cm, internal diameter - 75 μm, particle size - 3 μm, pore diameter - 120 A, pre-column: sorbent - Aeris Peptide XB-C18, (Agilent, USA), length - 1 cm, internal diameter - 100 μm, particle size - 3 μm, pore diameter - 120 A, solvent A - 98.9% H2O, 1% MeOH, 0.1% formic acid; solvent B - 99.9% ACN, 0.1% formic acid), the chromatographic columns were thermostatted at 50°C. On the pre-column, application and washing were carried out for 10 minutes at a flow rate of 2 μl/min of solvent A. Separation was carried out at 300 nl/min, gradient: 1 min – 95% solvent A, 5% solvent B; The acetonitrile content was then increased linearly over 120 minutes to 60% solvent A and 40% solvent B. The chromatographic system was then washed with 95% solvent B for 10 minutes, followed by a 17-minute wash with 95% solvent A and 5% solvent B. Mass spectral acquisition mode: mass spectral acquisition time – 250 ms, mass/charge ratio range from 300 to 1250 m/z, criteria for preferential selection of ions for isolation and fragmentation – charge 2-5, the number of parent ions sampled in each cycle – no more than 50, minimum intensity – 100 counts/s. After the first analysis, the ion was forcibly excluded from the list of ions for fragmentation for 15 s. Fragmentation parameters: fragmentation spectra accumulation time – 100 ms, mass/charge ratio range from 100 to 2000 Th, voltage in the collision cell varied linearly from 25 V to 55 V, full cycle time – no more than 5.3 s."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Raw LC-MS/MS data from the Q Exactive HF-X mass spectrometer were converted to .mgf peak lists with MSConvert (ProteoWizard Software Foundation). For this procedure, we used the following parameters: “--mgf --filter peakPicking true [1,2]”. For a thorough protein identification, the generated peak lists were searched with MASCOT (version 2.5.1, Matrix Science Ltd., UK) and X! Tandem (ALANINE, 2017.02.01, The Global Proteome Machine Organization) against the UniProt Knowledgebase (taxon human) with the concatenated reverse decoy dataset. The precursor and fragment mass tolerance were set at 20 ppm and 50 ppm, respectively. The database search parameters included no enzyme or possible post-translational modification (PTM). For X! Tandem, we also selected parameters that allowed us to quickly check for protein N-terminal acetylation, peptide N-terminal glutamine ammonia loss or peptide N-terminal glutamic acid water loss."],"omics_type":["Proteomics"],"labhead":["Georgij Arapidi"],"instrument_platform":[""],"labhead_affiliation":["Head of System Biology Lab. at Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency"],"submission_type":["COMPLETE"],"species":["Homo Sapiens (human)"],"submitter_mail":["arapidi@gmail.com"],"publication":["Not available"],"submitter_affiliation":["System Biology Lab. at Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency"],"submitter_country":["Russia"],"doi":["10.6019/PXD077080"],"additional_accession":[]},"is_claimable":false,"name":"Adaptation of an immunoaffinity chromatography protocol for the isolation of the cell line immunopeptides","description":"BACKGROUND. For developing targeted immunotherapy against ovarian adenocarcinoma, direct identification of peptides presented by major histocompatibility complex class I (HLA I) on the surface of tumor cells can be utilized. However, standard immunopeptidomics protocols may vary substantially in their efficiency of immunopeptidome isolation depending on lysis conditions. Optimizing detergents for immunoaffinity purification of complexes enhances analytical sensitivity, expands the repertoire of identified ligands, and increases the likelihood of detecting clinically relevant peptides suitable for personalized immunotherapeutic approaches.AIM. To evaluate the effect of various detergents on the efficiency of identification of peptide ligands of HLA I complexes. METHODS. Immunopeptidome from cell lines were isolated using immunoaffinity chromatography and analyzed by liquid chromatography-mass spectrometry.RESULTS. In this study, we tested an affinity chromatography-based immunopeptidome isolation protocol, comparing various detergents (CHAPS, NP-40, SOD, and Triton X-100) for cell lysis, and observed no statistically significant differences in the number of identified peptides.CONCLUSION. Each of the four tested detergents provides identification of unique sets of peptides.","dates":{"publication":"2026-04-15","submission":"2026-04-13"},"accession":"PXD077080","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:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:43186","NEWT:428146","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:399784","NEWT:96731","NEWT:383379","NEWT:1401257","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: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: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:145458","NEWT:633149","NEWT:1149786","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: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:1245466","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: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:128017","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:198107","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:6269","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:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:2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