{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/v08/MSV000096062/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Egor A. Repkin"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=8d3111a6f64b4e8eb12a277eb3b5bc0e"],"submitter_email":["erepkin53@gmail.com"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["20"],"ptm_modification":["UNIMOD:4 - \"Iodoacetamide derivative.\"","UNIMOD:7 - \"Deamidation.\"","UNIMOD:259 - \"13C(6) 15N(2) Silac label.\"","UNIMOD:1 - \"Acetylation.\"","UNIMOD:35 - \"Oxidation or Hydroxylation.\"","UNIMOD:267 - \"13C(6) 15N(4) Silac label.\""],"data_protocol":[""],"omics_type":["Proteomics"],"instrument_platform":["timsTOF Pro"],"species":["Homo Sapiens (ncbitaxon:9606)"],"submitter_affiliation":["Saint-Petersburg State University"],"name_synonyms":["BcDNA:GH04604, AA408225, vasoactive intestinal contractor, DmelCG14028, determination, Cyc, Cd144, VIc, total expressed protein, preproendothelin-2, EDN2, l(2)03771, valvular interstitial cell, cardiac valve interstitial cell, 7B4, VE-Cad, Cype, VEcad, cyc, chemical analysis, PPET2, VIC, COXVIc, 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carbonyldiamide, Hac-1, C18, cupric formate, chemical analysis, Step-Parent, Spinal Cord Injuries, MFS1, Sodium, chronic airway obstruction, chronic obstructive, aluminum formate, Sinusoidal, Mass Spectrum Analyses, XKrk1, AU020952, ensemble, Separations, GR-RBP7, GR-RBP8, ethanenitrile, Interleukin-1 beta-converting enzyme, 2-Amino-3-mercaptopropionic acid, SSKS., plan specification, Computer Programs, Capillary Beds, C-Kit, Endothelial Cell, Fees, chronic obstructive lung disease (disorder), E920, COXVIc, Methoxide, Spinal Cord Contusion, channel-forming toxin activity, Pilot, T22F8.160, Meth, NCMe, Chronic Airflow Obstructions, DmelCG6829, Data File, Pp1, PILOT, zinc formate, cleavage, CG7788, High Performance Liquid Chromatography Mass Spectrometry, crice, lead salt, protein, preproendothelin-2, Molecular Biologies, High Performance Liquid Chromatography-Mass Spectrometry, peptide, Hydrolase, L-Isomer Methionine, ammonium tetraformate, Machine Readable Data Files, Liquid Chromatography-Mass, peptido, valva aortae, Propylene, Lymphatic Endothelial Cell, Apaf1, Cystein, valvular endothelial cell, Chronic Obstructive Pulmonary Disease (COPD), protein aggregate, methyl ketone, l(3)j5D5, wood alcohol, 24B, COLD (chronic obstructive lung disease), LCMSMS, peptides, Biology, NEC in ICD9CM_2006, TAF-I, E927b, Open, arc, mAPC, Proteolytic, ark, T1, Chronic airflow limitation, anatomical valve, l(3)j5B5, l(2)03771, IGAAD, pp1-13C, lithium salt, DmelCG10574, ICE, GLYCINE RICH PROTEIN 7, Bio-Informatics, ppm, MKL, blood capillary, dihydrogen oxide, Sl, GPHYSD2, ammonium (2:1) salt, Sinusoid, CHRONIC, obstructive lung disease, Spinal Cord Trauma, Alcohol, iCE, D-Apaf-1, drice, Cyc, Step Parents, dimethylketone, 2-Amino-4-(methylthio)butyric acid, Dmel_CG7826, StF-IT-1, Tr-kit, Th, Stepparent, Cys, Airflow Obstructions, Source Softwares, Spectroscopy, drIce, SZ1, cyc, CHRONIC OBSTRUCTIVE, Computer Applications Softwares, cavum oris, Data Linkage, KIT, WASH, CG14784, nickel (+2) salt, Dmel_CG7835, Co-Pilots, Crystal, CG14783, CHRONIC OBSTRUCTIVE LUNG DIS, MNB, tyrosine-protein kinase Kit, Persorb, Christmas Island (Australia), ammonium salt, Parent, P45, cobaltous formate, CG4299, AW124434, acqua, L-Cystein, Wood, apaf-1, COPD - Chronic obstructive pulmonary disease, copper salt, p45, Qed-1, Liquid, Wasser, i2pp2a, 1728, Cysteine Hydrochloride, Dapaf-1/HAC-1, XAD-2 resin, P62, cesium salt, SCF receptor activity, Spectrum Analyses, Computer, Database, Methylalkohol, Vascular Endothelial, PHAPII, TIPS, Russian SFSR, Protein Sequence Databases, Cold, Hac1, polypeptide chain, Homo sapiens, ECTOL1, 14C-labeled, p63, p65, Mass, Co-Pilot, Wood Alcohol, Pro-Mega, study, Cold Temperatures, Ultra-Performance Liquid Chromatography-Mass Spectrometry, Fdc, Data Retrieval, Glass, poly(styrene-divinylbenzene), copoly(styrene-divinylbenzene), ipp2a2, dapaf-1, Acetylations, SWISS PROT, dapaf, calcium formate, Charges, Fee, 10^[-6], wood naphtha, Protein Structure, Ages, Capillary Endothelial Cell, VEC, Azeton, VECD, 2-iodo-, Applications Software, Open Source, COAD - Chronic obstructive airways disease, DYRK1, Computer Software, DL-Methionine, protein complex, clone 2.39, igaad, cell cycle quiescence, Transjugular Intrahepatic Portosystemic, strontium salt, group, echography, LC/MS/MS, water, I2PP2A, Dyrk1, CES2A1, Dark, Amino Acid Sequence Databases, buccal cavity, ACETONITRILE, Data Base, who, Temperature, Mass Spectrum, c-KIT, PRSS, CC1, Tripcellim, L-2-Amino-3-mercaptopropionic acid, Data Files, dApaf-1/DARK/HAC-1, sample population, chromic formate, retina autoimmune disease, lung MKs, Protein Gene Products, Interleukin-1 beta convertase, stationary phase, dSET/TAF-Ibeta, 2610030F17Rik, Russian S.F.S.R., concentration, Data, ultrasound, SSKS, 3.4.22.36, calcium salt, alpha-amino-gamma-methylmercaptobutyric acid, VIC, qkr[93F], Qa-1, cold (chronic obstructive lung disease), PP1alpha-13C, Chronic Obstructive Lung Disease, PP1-13C, CG32810, dAPAF-1, Qa1, Endothelial Cells, Protein Structure Database, Size, vasoactive intestinal contractor, IL1BC, cadmium salt, MeCN, Proteolytic Enzyme, VIc, BOUND WATER, chronic obstructive pulmonary disease (COPD), Basodexan, sci, Information Extraction, oxidane, Data Storage, Esteroproteases, 5730420M11Rik, 2-Propanone, Protein Databases, Polypeptides, protein polypeptide chains, KL receptor activity, cobalt(II) formate dihydrate, CH3-C#N, Chronic irreversible airway obstruction, How, echotomography, GRP8, GRP7, Prolene, Software Engineering, Proteases, bis(p-chlorophenyl)acetic acid, Il1bc, Gsfsow3, Divorced, DmelCG14028, DmelCG13176, CAFL - Chronic airflow limitation, proteins, Divorces, Lymphatic Endothelial Cells, IL-1BC, Data Storage and Retrieval, adult mouth, Computational, EG:196F3.2, AI047805, Bed, set, ultrasonic diagnosis, column, disease (COPD), T18c(37), sample, stage, Sequence Databases, Half Cystine, Computational Molecular Biologies, CG18323, PP1alpha13C, l(2)SH0173, 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activity, (R)-2-amino-3-mercaptopropanoic acid, CD117, X-ray, ME-IV, Gene Proteins, Peptidase, Applications Softwares, Rima oris, Ssm, xkl-1, LC-MS, liquid chromatography tandem mass spectrometry, [OH2], chronic obstructive pulmonary disease, liquid chromatography tandem mass spectroscopy, Hac-1/Dark, Bru, IPP2A2, E 920, determination, and rna binding 2, Protein Sequence Database, Xkl-1, Gsfsco1, cardiac valve interstitial cell, Methionine, exact), Lymphatic, Hostalen, chronic obstructive airways disease NOS (disorder), PP1, Min, Gsfsco5, ARK, Computer Program, DmelCG42273, SOW3, Mass Spectrum Analysis, Svc, Man (Taxonomy), vestibulum oris, Vascular Endothelial Cell, cisteina, mouth cavity, min, Computer Programs and Programming, purification, copper, CG10293, Bio-Informatic, Files, Proteinases, 13C, Capillary Endothelial, Ice, VEcad, Liquid Chromatography-Mass Spectrometries, T18c, dihydridooxygen, radionuclide imaging, dApaf1, Sodium Methoxide, glycine-rich RNA-binding protein 8, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, Racemethionine, EGR-3, Information Retrieval, 37b, 37c, phapii, 0904/17, Proteinase, ice, Modern, LC-MS/MS, aqua, Polymers, Aceton, ur, Programs, pulmonary disease (COPD), EDN2, Program, carbamide, Shunt, 7B4, Ionen, drICE, chronic obstructive pulmonary disease and allied conditions, Chronic airway disease, kl1-A, Propene, NOS, ET-2, Softwares, Carbinol, COPD NOS, carbinol, Mnb, parent ion, Chronic airway obstruction, Machine-Readable Data File, CHARGES, Empore, Bioinformatic, cold, hydrogen hydroxide, L-Cysteine, kit, hac1, MASS, Endothelial, DmelCG9156, beta-Ketopropane, dapaf-1S, Chronic Airflow Obstruction, H2NC(O)NH2, Post-Traumatic Myelopathy, dapaf-1L, Charge, precursor ion, Acetamide, chronic obstructive airways disease, anon-EST:Liang-2.39, Machine-Readable Data, Polypeptide, obstructive pulmonary disease (COPD), Proteomes, chronic obstructive lung disease, COLD, Traumatic Myelopathy, BcDNA:GH04604, human being, Canton and Enderbury Islands, DISEASE (COPD), L Isomer, FBN, Gene, Methyl, Protease, circadian rhythm, LC-MS-MS, formic acid, Dark/Hac-1/dApaf1, Karbamid, method, potassium salt, Dark/Hac-1/dApaf-1, Pulmonary Disease, scfr, Vascular, method used in an experiment, Harnstoff, Tina, L-Methionine, Del(8)44H, roentgenography, SCFR, Separated, valve, Pedameth, Mass Spectroscopy, Portosystemic Shunt, l(3)s2612, iones, dark, eau, Chronic Obstructive, OCTD, valvular interstitial cell, DARK, taf-ibeta, pharyngeal valve, DmelCG10293, Structure Database, cromium (+3) salt, Vec, Chromatography-Mass Spectrometries, dArk, Dapaf-1, sodium formate, COPD, Dimethylketon, Molecular Biology, nickel formate, 3H-labeled, 弁 (Japanese, not elsewhere classified, Parental, total expressed protein, strontium formate, apaf1, Extraction, PULM DIS CHRONIC OBSTRUCTIVE, Peptide, Bioinformatics, Chronic obstructive pulmonary disease finding (finding), Software Tool, capillary vessel, natural protein, Protein, GLYCINE-RICH RNA-BINDING PROTEIN 7, Software, CG14028, Dark/Apaf-I, Zystein, cyanomethane, WMS2, CG13176, chronic obstructive airway disease, DDA, Separation, uree, Aviator, 2-amino-3-sulfanylpropanoic acid, Dops, Engineering, Databases, Who/How, Trypure, Lymphatic Endothelial, c-kit, H-2T23, Ion, wood spirit, Modern Man, Chromatography-Mass Spectrometry, PPET2, Peptid, assay, SCI, Structure Databases, AA407739"],"additional_accession":["PXD056722"]},"is_claimable":false,"name":"Analysis of changes in the proteome of VIC and VEC cells co-cultured using SILAC medium","description":"Here we present data from a pilot experiment for co-culturing valve interstitial cells (VIC) and valve endothelial cells (VEC) in SILAC medium and analyzing changes in VIC and VEC proteome to study osteodifferentiation in the aortic valve.\nProtein isolation.\nThe RIPA solution with cells was exposed to ultrasound (2 times for 20 minutes with intermediate incubation on ice for 10 minutes) for protein extraction. Then protein was precipitated by 4 volumes of iced cold acetone (LC-MS Grade; LiChrosolv) and washed with methanol (LC-MS Grade; LiChrosolv). Protein pellet was air-dried and resuspended in 8 M urea (Sigma Aldrich, St. Louis, MO, USA) in 50 mM ammonium bicarbonate (Sigma Aldrich, St. Louis, MO, USA). \nSample preparation for shotgun proteomics.\nProtein concentrations were measured by Qubit 2.0 fluorimeter (Thermo Fisher Sci, Waltham, MA, USA) with QuDye Protein Quantification Kit (Lumiprobe, Moscow, Russia). 15 mkg of each sample were used for further LC-MS/MS analysis. Samples were incubated for 1 h at 37C with 5 mM DTT (Sigma Aldrich, St. Louis, MO, USA) with subsequent incubation in 15 mM iodoacetamide (Sigma Aldrich, St. Louis, MO, USA) for 30 min in the dark at room temperature, followed by quenching with 5 mM DTT. The samples were diluted with seven volumes of 50 mM ammonium bicarbonate and incubated for 17 h at 37C with Trypsin Gold in ratio 1:50 (Promega, Madison, WI, USA). Tryptic peptides were desalted by solid-phase extraction using stage-tips (Rappsilber et al., 2007) cording to standard protocol (Mamontova et al., 2019). Stage-tips were prepared by filling of polypropylene Vertex pipette tips (200 mkl; SSIbio, USA) with six layers of C18 reversed phase excised from Empore 3M C18 extraction disks (3M-Corporation, Maplewood, MN, USA). The desalted peptides were evaporated in a Labconco Centrivap Centrifugal Concentrator (Labconco, USA) and dissolved in water/0.1% formic acid (LC-MS Grade; LiChrosolv) to approximate final concentration of 250 ng/mkl for further LC-MS/MS analysis.\nLC-MS/MS analysis.\nApproximate 500 ng of peptides were used for shotgun proteomics analysis by LC-MS/MS with ion mobility in TimsToF Pro mass spectrometer (Bruker Daltonics, Bremen, Germany) with nanoElute UHPLC system (Bruker Daltonics, Bremen, Germany). UHPLC was performed in one-column separation mode with Aurora Ultimate 25 cm separation column (C18 stationary phase, length 250 mm, diameter 0.075 mm, particle size 1.7 mkm, pore size 120 A; IonOpticks, Fitzroy, Australia) in gradient mode with 300 nL/min flow rate with column temperature at 60C. Phase A was water/0.1% formic acid, phase B was acetonitrile/0.1% formic acid (LC-MS Grade; LiChrosolv). The gradient was from 2% to 18% phase B for 44 min, then to 25% of phase B for 11 min, then to 37% of phase B for 5 min, then to 85% of phase B for 2 min with subsequent wash with 85% phase B for 15 min. The column was equilibrated with 4 column volumes before each sample. Parameters of ion source for electrospray ionization: 4500 V of capillary voltage, 3 l/min N2 flow, and 180C source temperature. The mass spectrometry acquisition was performed in DDA PASEF mode in positive polarity with the fragmentation of ions with at least two charges in m/z range from 100 to 1700 and ion mobility range from 0.60 to 1.60 1/K0.\nDDA-PASEF raw data files were analyzed in Peaks Xpro software (v.10.6) (Bioinformatics Solutions Inc., Canada) using human protein SwissProt database (uploaded on 19 January 2024). The search parameters are as follows: trypsin/P protease; 2 possible missed cleavage sites; maximum number of variable modifications on a peptide was set to 2; 13C(6) 15N(4) SILAC label, 13C(6) 15N(2) SILAC label, methionine oxidation, N-term acetylation, NQ-deamidation, carbamidomethylation on cysteine were possible modifications; precursor charge range from 2 to 7; parent mass error tolerance 10.0 ppm, fragment mass error tolerance 0.05 Da; FDR 1%.","dates":{"publication":"Fri Oct 11 03:41:00 BST 2024"},"accession":"MSV000096062","cross_references":{}}