{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j42649.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j44087.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j42645.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j45415.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j44091.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j45399.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j42648.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j42643.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j44089.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j44093.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j42642_190924170651.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j45413.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j45417.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j45397.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j45395.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/j42646.raw"],"Mzid":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/465459_j45397_Shiro3Seq.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/412375_j42642_190924170651_SI.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/412378_j42646_SI.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/465456_j45415_Shiro3Seq.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/465457_j45399_Shiro3Seq.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/436542_j44093_ShiroHumLFQ.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/465458_j45395_Shiro3Seq.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/465454_j45417_Shiro3Seq.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/412376_j42643_SI.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/412379_j42648_SI.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/436543_j44087_ShiroHumLFQ.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/465455_j45413_Shiro3Seq.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/412374_j42649_SI.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/412377_j42645_SI.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/436541_j44091_ShiroHumLFQ.mzIdentML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD024234/436544_j44089_ShiroHumLFQ.mzIdentML"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["joao_paulo@post.harvard.edu"],"submitter":["Joao Paulo"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":[""],"submitter_keywords":["Macromolecule biogenesis","Metasome"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD024234"],"sample_protocol":["Protein preparation of mass spectrometry analysis. For identification of proteins in nuclear extracts, nuclear extracts were precipitated with trichloroacetic acid (TCA) to desalt and remove outer compounds, such as Triton X-100, that are found in the extraction buffer. Nuclear extracts were mixed with 100% TCA to a final volume of 12.5% TCA and incubated overnight. The   proteins were precipitated by centrifugation at 14,000 rpm for 10 min. TCA precipitation was followed by one acetone and one methanol wash (1 mL each with centrifugation at 14,000 rpm for 10 min) which were performed prior to protease digestion.   All samples precipitated nuclear extracts, as well as proteins derived from the immunoprecipitations, were resuspended in 100µL of 100 mM HEPES, pH 8.5 and digested at 37°C with trypsin at a 100:1 protein-to-protease ratio overnight. The sample was desalted via StageTip, dried via vacuum centrifugation, and reconstituted in 5% acetonitrile, 5% formic acid for LC-MS/MS processing."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["Data analysis. Mass spectra were processed using a Sequest-based in-house software pipeline. Spectra were converted to mzXML using a modified version of ReAdW.exe. Database searching was performed using a 50-ppm precursor ion tolerance for total protein level analysis. The product ion tolerance was set to 0.03 Da. These wide mass tolerance windows were chosen to maximize sensitivity in conjunction with Sequest searches and linear discriminant analysis 1, 2. Oxidation of methionine residues (+15.995 Da) was set as a variable modification. Peptide-spectrum matches (PSMs) were adjusted to a 1% false discovery rate (FDR). PSM filtering was performed using a linear discriminant analysis, as described previously, while considering the following parameters: XCorr, ΔCn, missed cleavages, peptide length, charge state, and precursor mass accuracy. PSMs were identified, quantified, and collapsed to a 1% peptide false discovery rate (FDR) and then collapsed further to a final protein-level FDR of 1%. Moreover, protein assembly was guided by principles of parsimony to produce the smallest set of proteins necessary to account for all observed peptides."],"omics_type":["Proteomics"],"labhead":["Joao A. Paulo"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Cell Biology Harvard Medical School USA"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["joao_paulo@post.harvard.edu"],"submitter_affiliation":["Harvard Medical School"],"submitter_country":["United States"],"sample_synonyms":["sodium salt, liquid chromatography tandem mass spectroscopy, Triton X-45, ammonium formate, Acide trichloracetique, 13C-labeled, MeCN, cadmium salt, nickel formate dihydrate, NCMe, lead formate, Triton X-305, aluminum salt, cesium salt, zinc formate, Gene, Octoxinols, Triton X305, Methyl, HEPES Monosodium Salt, lead salt, CH3OH, protein, magnesium formate, protein-containing complex, Methylalkohol, 2-ethanediyl), zinc salt, trichloro-, Poly(oxy-1, CG7826, Buffer, formic acid, 2-Propanone, propanone, potassium salt, ammonium tetraformate, Octoxynols, Octylphenoxy, cobalt(II) formate dihydrate, p63, 14C-labeled, Triton X 305, CH3-C#N, p65, LC-MSMS, dimethylcetone, Gene Products, CG7835, 1, CG42273, Octoxynol 9, Wood Alcohol, 3, Min, protein aggregate, trichloracetique, methyl ketone, DmelCG42273, wood alcohol, Octoxynol-9, HEPES Monosodium, FAM39E, LCMSMS, thallium (+1) salt, Rubidium, DmelCG13176, Monosodium Salt, Salt, beta-Trypsin, rubidium salt, min, ORF19, mAPC, copper, calcium formate, methanoic acid, alpha-(4-(1, Trichloroacetic, AI047805, lithium salt, Octylphenoxypolyethoxyethanols, Triton X45, Propanon, 1-Piperazineethanesulfonic acid, wood naphtha, sample, Sodium Trichloroacetate, LC-MS-MS., N-2-Hydroxyethylpiperazine-N'-2'-ethanesulfonic Acid, cromium (+3) salt, Azeton, Sodium Methoxide, Dimethyl ketone, 4-(2-hydroxyethyl)-, ammonium (2:1) salt, Octylphenoxy Polyethoxyethanol, sodium formate, nickel salt, LC-MS2, DYRK1, Dimethylketon, Alcohol, 1-(14)C-labeled, nickel formate, 3H-labeled, cobalt (+2) salt, protein complex, dimethylketone, Proteins, Octoxinol, LC-MS/MS, Dmel_CG7826, strontium formate, Methyl alcohol, potassium formate, copper (+2) salt, acetonitrile, strontium salt, buffer, Triton X100, Aceton, Triton X-100, Triton X 100, Wash2, Wash1, LC/MS/MS, sodium (4:1:1) salt, native protein, Pyroacetic ether, Dm1, magnesium salt, cupric formate, Protein, Trichloroacetate, Sodium, Rubidium Trichloroacetate, Dyrk1, MeOH, 1110049F14Rik, Vacuums, WASH, aluminum formate, nickel (+2) salt, Carbinol, ACETONITRILE, Acetic acid, Dmel_CG7835, cyanomethane, CG13176, carbinol, Mnb, MNB, AU020952, Acid, ammonium salt, lithium formate, PRSS, Triton X 45, CC1, formate, Tripcellim, cobaltous formate, N 2 Hydroxyethylpiperazine N' 2' ethanesulfonic Acid, cromium (+3), ethanenitrile, AW124434, beta-Ketopropane, beta Trypsin, sample population, chromic formate, ME-IV, Protein Gene Products, Gene Proteins, Trypure, Wood, Acide, spirit of wood, liquid chromatography-tandem mass spectroscopy, wood spirit, copper salt, ammonium (4:1) salt, calcium salt, liquid chromatography tandem mass spectrometry, 3-tetramethylbutyl)phenyl)-omega-hydroxy-, HEPES, methyl cyanide, lead (+2) salt, Polyethoxyethanol, Methyl Alcohol, Methoxide"],"name_synonyms":["polymer, macromolecules, Human, macromolecular complex, human being, polymer molecule, Man (Taxonomy), Homo sapiens, protein complex, Modern Man, Modern, protein containing complex, Cell., macromolecule complex, protein, protein aggregate, protein-containing complex, macromolecule, polymers, Man, human, protein-protein complex"],"data_synonyms":["SH2-Bb, IPP2A2, SH2 domain-containing protein 1B, 2-amino-4-(methylsulfanyl)butanoic acid, determination, unsegmented paraxial mesoderm, L Isomer, Irip, FBN, Gene, protein, precursor, broad, protein-containing complex, somitomeric mesoderm, GCPII, NAALAdase, PHAPII, Discriminant, 5730420M11Rik, peptide, Polypeptides, NAALADase I, L-Isomer Methionine, FOLH, Methionine, peptido, ECTOL1, sensitive, Gene Products, L-Methionine, N-acetylated-alpha-linked acidic dipeptidase I, C530001K22Rik, mKIAA1299, 3.4.17.21, Analysis, protein aggregate, sensitivity, WMS, Pedameth, SH2-B, somitogenic mesoderm, SET, SH2B, peptides, Analyses, Membrane glutamate carboxypeptidase, TAF-I, M, ipp2a2, 2pp2a, mGCP, NAALAD1, CG10574, Folylpoly-gamma-glutamate carboxypeptidase, OCTD, DmelCG4299, allergic reaction, IGAAD, set, data processing, 2PP2A, 2-amino-4-(methylthio)butanoic acid, 10^[-6], DmelCG10574, taf-ibeta, ppm, dSET, dSet, Sensitivity, peptidos, GPHYSD2, metionina, Racemethionine, z, SGS, phapii, wide/broad, DL-Methionine, unsegmented mesenchyme, protein complex, Proteins, igaad, 2-Amino-4-(methylthio)butyric acid, StF-IT-1, L-Isomer, SH2-B PH domain-containing signaling mediator 1, Peptide, group, GCP2, ACMICD, GIG27, Glutamate carboxypeptidase II, polypeptide, Cell growth-inhibiting gene 27 protein, native protein, I-2PP2A, PSM, Psm, chemical analysis, Dm I-2, Protein, I2PP2A, MFS1, Methionin, Hmet, segmental plate, Prostate-specific membrane antigen, presumptive somite mesoderm, Mopsm, Sh2bpsm1, WMS2, Data Base, Met, parent ion, Pteroylpoly-gamma-glutamate carboxypeptidase, PH and SH2 domain-containing signaling mediator, HLA-DR-associated protein II, ensemble, DI-2, I-2Dm, FGCP, Specificity, MASS, CG4299, Folate hydrolase 1, I-2PP1, Protein Gene Products, Pro-rich, Gene Proteins, data analysis, dSET/TAF-Ibeta, wide, 2610030F17Rik, TAF-IBETA, precursor ion, Specificity and Sensitivity, Data, Discriminant Analyses, SSKS, AI425885, alpha-amino-gamma-methylmercaptobutyric acid, PSMA, Peptid, TAF-Ibeta, assay, Polypeptide, AA407739, i2pp2a, Liquimeth, Peptide., Data Analyses"],"description_synonyms":["polymer, macromolecules, Human, macromolecular complex, human being, polymer molecule, Man (Taxonomy), Homo sapiens, protein complex, Modern Man, Modern, protein containing complex, Cell., macromolecule complex, protein, protein aggregate, protein-containing complex, macromolecule, polymers, Man, human, protein-protein complex"],"additional_accession":[]},"is_claimable":false,"name":"RNAmetasome, a multi-protein complex for the macromolecule biogenesis in human cells","description":"The RNAmetasome, a multi-protein complex for the macromolecule biogenesis in human cells, is defined and 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