Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1028.tandem.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1045.tandem.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1027.tandem.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1037.tandem.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1037.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1045.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1028.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1027.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1027.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1028.mzid_P1028.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1027.mzid_P1027.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1037.mzid_P1037.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1045.mzid_P1045.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1037.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1045.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1028.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1037.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1027.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1045.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1028.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1045.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1028.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1027.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077095/P1037.datprimaryOK200arapidi@gmail.comGeorgij ArapidiImmunopeptidomicsData-dependent acquisitionMass SpectrometryMalignant Neoplasm Of Ovaryhttps://www.ebi.ac.uk/pride/archive/projects/PXD077095OvaryMalignant CellTumors used.This study utilized ovarian adenocarcinoma tumor tissue samples from patients who had undergone chemotherapy with taxanes and carboplatin (n = 3, patients 1-3) and without prior treatment (n = 1, patient 4). Samples were obtained from the Russian Research Center of Roentgenology and Radiology (Moscow, Russia). Diagnoses were confirmed by morphological examinations. The study was approved by the Ethics Committee of the Russian Research Center of Roentgenology and Radiology (Agreement and Protocol No. 30-2018/E dated November 13, 2018). All patients provided written consent to participate.Preparation of tissue lysates.For tumor tissue, a 0.2 g sample was homogenized with ceramic beads (MagNA Lyser Green Beads, Roche, 03358941001, Switzerland) in 1 ml of lysis buffer (150 mM NaCl, 50 mM Tris-HCl, Protease Inhibitor Cocktail X100, 1% NP-40) using an automated homogenizer (MagNA Lyser, Roche) at 7000 g with periodic sample cooling. The tissue homogenate, along with the ceramic beads, was transferred to 4 ml of lysis buffer and left in a multirotator (BioSan Multi-Bio RS-24) for 1 hour at 4°C. The resulting tissue lysate was pre-sonicated for 5 minutes (Elma S30H ultrasonic bath), centrifuged for 15 minutes 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 a Pierce Protein A/G Agarose resin suspension (Thermo Fisher, 20422) was loaded onto 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. Before loading, the cell medium was diluted 1:1 with PBS. The column was washed with 5 ml of 150 mM NaCl and 50 mM Tris-HCl. The tumor lysate was then 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 work, the column 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 min (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.PrideRaw 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.ProteomicsGeorgij ArapidiHead of System Biology Lab. at Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological AgencyCOMPLETEHomo Sapiens (human)arapidi@gmail.comNot availableSystem Biology Lab. at Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological AgencyRussia10.6019/PXD077095falseIdentification of major histocompatibility complex class I ligands in ovarian adenocarcinoma tumorsBACKGROUND. 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.AIM. To identify ligands of HLA I of ovarian adenocarcinoma tumors. METHODS. Immunopeptidome from postoperative material of patients with ovarian adenocarcinoma were isolated using immunoaffinity chromatography and analyzed by liquid chromatography-mass spectrometry.RESULTS. Using NP-40, 5 peptides belonging to the proteins of cancer/testis antigens (CTA) were identified in the immunopeptidomes of postoperative material from patients with ovarian adenocarcinoma, 3 of which, according to the human protein atlas, are indeed not expressed in normal ovarian tissues.CONCLUSION. Immunopeptidome analysis allows the identification of peptides of CTA proteins, but a larger sample of postoperative material from patients with ovarian adenocarcinoma and experimental testing of the immunogenicity of the identified peptides are needed for further 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