{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/v01/MSV000079301/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Sylwia Kedracka-Krok"],"instrument_platform":["micrOTOF-Q II"],"species":["Mus Musculus (ncbitaxon:10090)"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=3346ba26431043c3ae70ffa5f3bfcb08"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["4"],"ptm_modification":["UNIMOD:4 - \"Iodoacetamide derivative.\"","UNIMOD:7 - \"Deamidation.\"","UNIMOD:35 - \"Oxidation or Hydroxylation.\""],"data_protocol":[""],"pubmed_abstract":["<h4>Background</h4>The cell nucleus is a highly dynamic subcellular compartment performing crucial processes for functioning and administration of the cell. Proteomic analysis of isolated nuclear fraction enables in-depth insight into these processes leading to better understanding of physiological and pathological state of the brain. There is no universal method for nuclear proteome investigation and each biological material needs individual optimization. An additional difficulty is the large amount of nucleic acids, which impairs isoelectrofocusing of proteins and shotgun mass spectrometry analysis of complex peptide samples.<h4>New method</h4>We performed the first comprehensive optimization of intact nuclei isolation from mouse brain in combination with nuclear protein purification prior to two-dimensional gel electrophoresis (2DE) and gel-free proteomic analysis.<h4>Results</h4>Application of sonication, digestion with nuclease and protein precipitation with acetone allowed to obtain high quality 2DE gels. Shotgun mass spectrometry analysis of isolated proteins proved an enrichment in nuclear proteins. The 66.4% of 265 identified proteins had assigned nucleus localization in UniProt database. Gene Ontology analysis using DAVID platform revealed the highest fold enrichment in spliceosome (24.5), nuclear periphery (12.4) and nuclear matrix (11.3).<h4>Comparison with existing methods</h4>The proposed procedure is tailored to mouse brain tissue nuclear subproteome investigation. The quality of isolated nuclei, the effectiveness of the protein purification, efficiency of protein recovery after precipitation and overall method reproducibility was taken into detailed consideration.<h4>Conclusions</h4>The elaborated procedure could be further applied for in-depth proteomic analysis of molecular processes occurring in the mouse brain nucleus."],"pubmed_title":["Optimized procedure of extraction, purification and proteomic analysis of nuclear proteins from mouse brain."],"pubmed_authors":["Jankowska Urszula U, Latosinska Agnieszka A, Skupien-Rabian Bozena B, Swiderska Bianka B, Dziedzicka-Wasylewska Marta M, Kedracka-Krok Sylwia S"],"name_synonyms":["the brain, Mus musculus, Nuclear Protein, suprasegmental structures, determination, Laboratory, Swiss, mice, Mus domesticus, Proteins, mouse, Swiss Mouse, House Mice, Swiss Mice, Nucleolar Proteins, suprasegmental levels of nervous system, House Mouse, encephalon, Encephalon., domesticus, Laboratory Mice, House, Mus, Nucleolar Protein, chemical analysis, Protein, Mus musculus domesticus, Nuclear, Mouse, synganglion, assay, house mouse, Nucleolar, Mice, Laboratory Mouse"],"pubmed_title_synonyms":["the brain, Intervention Strategies, suprasegmental structures, Procedures, Laboratory, Mus domesticus, Proteins, mouse, Procedure, House Mouse, encephalon, Intervention or Procedure, Techniques, isolation, House, Mus, Method, Nucleolar Protein, Protein, proteomic analysis, Studies, Mus musculus domesticus, Nuclear, synganglion, Mice, Technique, Intervention, Mus musculus, Nuclear Protein, interventionDescription, Swiss, mice, Swiss Mouse, Interventional, House Mice, Swiss Mice, purification, Nucleolar Proteins, Methodological, suprasegmental levels of nervous system, Methodological Study, SURGICAL AND MEDICAL PROCEDURES, Encephalon., domesticus, Laboratory Mice, Study, isolation and purification, Methodological Studies, Mouse, house mouse, Nucleolar, Laboratory Mouse"],"description_synonyms":["the brain, liquid chromatography tandem mass spectroscopy, Solubilities, IL1BC, Meth, Laboratory, popliteal pterygium syndrome, DrIce, DrICE, Mus domesticus, CASP-1, surfactants, CG7788, Gene, crice, 2-(indol-3-yl)ethanoic acid, PPS1, Chalk, House Mouse, LC-MS-MS, Agent, 2-Propanone, Surface-Active Agent, Polypeptides, propanone, IAA, peptido, House, LC-MSMS, dimethylcetone, Tina, Gene Products, Mus musculus domesticus, PpS, synganglion, Il1bc, Mice, cleft Lip/palate, methyl ketone, C62, DmelCG6525, Glass, LCMSMS, peptides, facio-genito-popliteal syndrome, Swiss, LPS, OFC6, Surface, Surface Active Agents, PCE-2, beta-Trypsin, PPS, Pps, Swiss Mice, Surface-Active, Indoleacetic acid, posterior pharyngeal sensilla, suprasegmental levels of nervous system, SKIP, FBgn0082831, IL-1BC, Amphiphilic, hpo, (indol-3-yl)acetic acid, Propanon, Caspase-1 subunit p20, ICE, Ice, cleft lip/palate paramedian mucous cysts of the lower lip popliteal pterygium digital and genital anomalies, n, peptidos, house mouse, Azeton, Dimethyl ketone, PIT, LC-MS2, paramedian mucous cysts of the Lower Lip, Dimethylketon, Organ X, suprasegmental structures, Caspase-1 subunit p10, iCE, ice, drice, caspase 3, Surfactant, dimethylketone, Active Agent, Proteins, mouse, LC-MS/MS, Spp, SPP, VWS1, CE-2, Surface Active, encephalon, Aceton, Peptide, DmelCG7788, (Indol-3-yl)acetate, LC/MS/MS, Pyroacetic ether, larval pharyngeal sense organ, Mus, drIce, drICE, Surfactants, Protein, spp, VWS, digital and genital anomalies, CES2A1, IES, Crystal, Mus musculus, 10^[-9], PRSS, mice, Encephalon, Active Agents, P45, Swiss Mouse, 3-Indolylessigsaeure, Tripcellim, popliteal pterygium, House Mice, IL-1 beta-converting enzyme, Interleukin-1 beta-converting enzyme, faciogenitopopliteal syndrome, beta-Ketopropane, beta Trypsin, domesticus, Laboratory Mice, Polio and Post-Polio Syndrome, Protein Gene Products, Interleukin-1 beta convertase, Speed, Gene Proteins, Trypure, heteroauxin, Agents, liquid chromatography-tandem mass spectroscopy, surface active agent, Tensides, Drice, 3.4.22.36, CG6525, Amphiphilic Agents, p45, liquid chromatography tandem mass spectrometry, Peptid, Mouse, Polypeptide, X-organ of Keilin, anatomical systems., DRICE, Laboratory Mouse, Tenside, Surface Active Agent"],"pubmed_abstract_synonyms":["projections, Gene Ontology Projects, determination, Laboratory, Ass-1, Mus domesticus, Mbp1, protein, House Mouse, localization of nucleus, Productivity, dmTAF[[II]]230, peptide, 2-Propanone, Polypeptides, Readability, Techniques, protein polypeptide chains, peptido, Method, spliceosome, Nucleolar Protein, AA408052, horsetail nucleus, DGS, Project, fold, synganglion, protein aggregate, myd, methyl ketone, Nucleus, Nuclear Protein, TFIID TAF250, peptides, cel, Scaffold, Tissue, Mbp-1, Swiss Mice, purification, proteins, procedures, suprasegmental levels of nervous system, establishment and maintenance of nucleus localization, free, SURGICAL AND MEDICAL PROCEDURES, isolation and purification, ASS, Nucleoskeletons, Methodological Studies, acidos nucleicos, Propanon, DmelCG1106, papilla, house mouse, spliceosome complex, Scaffolds, dTAF[[II]]230, suprasegmental structures, gyltl1b-b, Nuclei, dimethylketone, lamina, mouse, TAF200, flanges, TAFII-250, Procedure, TAF250/230, results, Aceton, Cell Nuclei, Nucleoskeleton, TAFII250, Pyroacetic ether, nucleic acids, MDDGA6, mKIAA0609, shelf, Nuclear Matrices, cell nucleus, Ontology Projects, simple tissue, KIAA0609, fg, Acid, Mus musculus, Gene Ontologies, Ontology, gyltl1b, Ontologies, Projects, mice, shelves, Sonications, Encephalon, mdc1d, Swiss Mouse, expanded, Methodological, CG17603, projection, TAF[[II]], Methodological Study, beta-Ketopropane, ridge, Nucleic, CG1106, domesticus, MDC1D, brain nuclei, enr, Taf250, enlarged, cell nucleus localization, SR3-5, Spliceosome, Acids, Mouse, Polypeptide, Proteomes, TAF230, the brain, big, d230, Procedures, lamellae, Nuclear Scaffold, Matrix, Gene, dTAFII250, nucleus localisation, protein-containing complex, Matrices, EfW1, process of organ, Gene Ontology Project, froggy, Gene Ontology, Gyltl1a, Intervention or Procedure, lamella, method, large, Electrophoreses, propanone, acides nucleiques, polypeptide chain, dmTAF1, isolation, House, Taf230, method used in an experiment, dimethylcetone, Studies, Gene Products, Mus musculus domesticus, Mice, Technique, TAF250, study, Taf200, dTAF[[II]]250, interventionDescription, cell, Swiss, MDDGB6, gel, Interventional, Taf1p, LARGE, ridges, Study, dTAF250, BPFD#36, great, peptidos, Azeton, TAF, laminae, Dimethyl ketone, Nuclear Scaffolds, Intervention Strategies, Dimethylketon, TAF[[II]]250, acide nucleique, protein complex, Proteins, total expressed protein, l(3)84Ab, BG:DS00004.13, encephalon, Cell, Peptide, dTAF230, brain nucleus., polypeptide, native protein, natural protein, Mus, p230, Nucleic Acid, Protein, chemical analysis, proteomic analysis, TAF[[II]]250/230, TFIID, NA, Nuclear, background, techniques, nucleoskeleton, flange, organ process, Data Base, Intervention, Taf[[II]]250, Ontology Project, TAF[[II]]230, Nukleinsaeure, House Mice, TAF[II]250, Nucleolar Proteins, acido nucleico, Understanding, introduction, Laboratory Mice, plan specification, Protein Gene Products, processes, Gene Proteins, DmelCG17603, Isolation of Nuclei TAgged in specific Cell Types, Nukleinsaeuren, Peptid, assay, Nucleolar, Laboratory Mouse, methodology, TAF1"],"citation_count":["0"],"additional_accession":["PXD002872"]},"is_claimable":true,"name":"Shotgun analysis of nuclear proteins from mouse brain","description":"Nuclei were isolated from the mouse brain. Proteins were extracted with addition of Bensonase and cleaned up by acetone precipitation. Proteis were resuspended in 50 mM ammonium bicarbonate and PPS Silent Surfactant. Samples were sonicated on ice to improve the solubility of proteins, then alkylated with IAA and digested with trypsin. Peptides were analyzed by LC-MS/MS using the UltiMate 3000RS nano-System coupled with microTOF_QII.","dates":{},"accession":"MSV000079301","cross_references":{"pubmed":["26698226"]}}