{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/sdrf.tsv"],"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_10fractions_combine.group.xml"],"Mzml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F4_5ul.mzml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F8_5ul.mzml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F10_5ul.mzml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F9_5ul.mzml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F3_5ul.mzml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F6_5ul.mzml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F2_5ul.mzml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F5_5ul.mzml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F7_5ul.mzml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_F1_5ul.mzml"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006542/160531_Tanju_RPRP_8plex_10fractions_combine.group"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":180,"searchCount":0},"additional":{"labhead_mail":["denchjs@nus.edu.sg"],"submitter":["Tanujaa Suriyanarayanan"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":["Not available"],"submitter_keywords":["Enterococcus faecalis","Biofilm","Proteome","Itraq"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD006542"],"sample_protocol":["100 µg of biofilm proteins extracted from the four E. faecalis strains in duplicates were subjected to trypsin digestion and labelled with iTRAQ Reagent 8-plex kit (AB SCIEX). The samples were then acidified and subjected to strong cation-exchange chromatography to remove all interfering substances. The eluted fractions eluted were desalted using Sep-Pak C18 cartridges (Water) followed by 2D LC-MS/MS analysis using 1290 Infinity LC system coupled with 1260 Fraction Collector."],"repository":["Pride"],"quantification_method":["iTRAQ"],"modification":["iTRAQ8plex-116 reporter+balance reagent acylated residue","monohydroxylated residue","acetylated residue","methylthiolated residue"],"data_protocol":["Peptide identification and quantification was carried out on the ProteinPilot 5.0 software Revision 4769 (AB SCIEX) using the ParagonTM database search algorithm (5.0.0.0.4767) and the integrated false discovery rate (FDR) analysis function. The data were searched against a protein sequence database downloaded from UniProtKB for E. faecalis 29212. A strict unused confidence score of >1.3 corresponding to a peptide confidence level of 95% was used as the selection criteria for proteins."],"omics_type":["Proteomics"],"labhead":["C J Seneviratne"],"instrument_platform":["TripleTOF 5600"],"labhead_affiliation":["Dentistry Dean's Office, National University of Singapore, Singapore"],"submission_type":["PARTIAL"],"species":["Enterococcus Faecalis (streptococcus Faecalis)"],"submitter_mail":["tan.suri@gmail.com"],"publication":["29358339 Suriyanarayanan T, Qingsong L, Teck Kwang L, Yew Mun L, Truong T, Seneviratne CJ. iTRAQ-based quantitative proteomics of strong and weak biofilm formers of Enterococcus faecalis reveals novel regulators of biofilm formation. Mol Cell Proteomics. 2018 10.1074/mcp.ra117.000461"],"curator_keywords":["Biomedical"],"submitter_affiliation":["National University of Singapore"],"pubmed_abstract":["Enterococcus faecalis is a bacterial pathogen associated with both endodontic and systemic infections. The biofilm formation ability of E. faecalis plays a key role in its virulence and drug resistance attributes. The formation of E. faecalis biofilms on implanted medical devices often results in treatment failure. In the present study, we report protein markers associated with the biofilm formation ability of E. faecalis using iTRAQ-based quantitative proteomics approach. In order to elucidate the biofilm-associated protein markers, we investigated the proteome of strong and weak biofilm-forming E. faecalis clinical isolates in comparison with standard American Type Culture Collection (ATCC) control strains. Comparison of E. faecalis strong and weak biofilm-forming clinical isolates with ATCC control strains showed that proteins associated with shikimate kinase pathway and sulfate transport were up-regulated in the strong biofilm former, while proteins associated with secondary metabolites, cofactor biosynthesis, and tetrahydrofolate biosynthesis were down-regulated. In the weak biofilm former, proteins associated with nucleoside and nucleotide biosynthesis were up-regulated, whereas proteins associated with sulfate and sugar transport were down-regulated. Further pathway and gene ontology analyses revealed that the major differences in biofilm formation arise from differences in metabolic activity levels of the strong and weak biofilm formers, with higher levels of metabolic activity observed in the weak biofilm former. The differences in metabolic activity could therefore be a major determinant of the biofilm ability of E. faecalis The new markers identified from this study can be further characterized in order to understand their exact role in E. faecalis biofilm formation ability. This, in turn, can lead to numerous therapeutic benefits in the treatment of this oral and systemic pathogen. The data has been deposited to the ProteomeXchange with identifier PXD006542."],"pubmed_title":["Quantitative Proteomics of Strong and Weak Biofilm Formers of Enterococcus faecalis Reveals Novel Regulators of Biofilm Formation."],"pubmed_authors":["Suriyanarayanan Tanujaa T, Qingsong Lin L, Kwang Lim Teck LT, Mun Lee Yew LY, Truong Thuyen T, Seneviratne Chaminda Jayampath CJ"],"sample_synonyms":["liquid chromatography tandem mass spectroscopy, LC-MS2, Kation, proto-oncogene c-Kit, determination, cation, Proteins, Sprain, Kationen, LC-MS/MS, SCF receptor activity, Gene, Tr-kit, Xkl-1, cationes, LC-MS-MS, PBT, KL receptor activity, LC/MS/MS, Gsfsco1, scfr, resilient, KIT ligand receptor activity, body system., tough, Protein, LC-MSMS, chemical analysis, Strain, Gene Products, SCO5, kl1-A, system, SCO1, KIT, connected anatomical system, Biofilm, Gsfsow3, Sprains, SCFR, Gsfsco5, Hydrogen Oxide, XKrk1, SOW3, tyrosine-protein kinase Kit, strong, pbt, c-KIT, Fdc, anatomical systems, LCMSMS, beta-Trypsin, Tripcellim, proteins, kit, W, CD117, beta Trypsin, Protein Gene Products, organ system, Gene Proteins, Trypure, cations, Sep-Pak C18, c-kit, C-Kit, liquid chromatography-tandem mass spectroscopy, Ssm, xkl-1, Bs, liquid chromatography tandem mass spectrometry, Cation, Strains, assay, Sl, Chromatographies, Strains and Sprains, krk1"],"pubmed_title_synonyms":["strong, count in organism, Micrococcus ovalis, resilient, Streptococcus liquefaciens, Peptidomics, tough, Streptococcus faecalis., Streptococcus Group D, weak, number, Enterococcus proteiformis, quantitative, Biofilm, Micrococcus zymogenes, presence, Streptococcus glycerinaceus, Enterocoque, presence or absence in organism"],"data_synonyms":["Applications Software, Open Source, data, Computer Software, determination, False, protein complex, selection process, Proteins, Gene, function, protein, Computer, protein-containing complex, Peptide, Source Softwares, Software Tools, Tool, Programs, polypeptide, peptide, Polypeptides, Program, Computer Applications, protein polypeptide chains, Software Tool, ClvPrd, peptido, native protein, natural protein, polypeptide chain, Algorithm, Computer Applications Software, chemical analysis, Protein, Computer Applications Softwares, Gene Products, sequence, Software Engineering, Softwares, protein aggregate, Software, Computer Program, Application, Data Base, Open Source Softwares, proportion, Software Applications, F, peptides, Protein., Source Software, Software Application, Open, Engineering, proportionality, Open Source Software, Computer Programs and Programming, rate, proteins, primary structure of sequence macromolecule, Computer Software Application, Protein Gene Products, Computer Programs, Gene Proteins, Applications, Applications Softwares, Tools, quotient, Peptid, peptidos, Polypeptide, assay, Computer Software Applications, ratio"],"description_synonyms":["associated., study, strong, resilient, tough, weak, Strain, Sprain, total expressed protein, Strains, associated, Biofilm, Sprains, Strains and Sprains, Proteomes"],"pubmed_abstract_synonyms":["sugar transport, Gene Ontology Projects, Activity, Peptidomics, Streptococcus Group D, drug susceptibility/resistance, number, Infestations and Infections, secondary metabolites, Gene, Enterococcus proteiformis, biosynthesis, protein, protein-containing complex, aroL protein, infectivity, presence, dIKK-gamma, SO4(2-), Gene Ontology Project, Failure, Gene Ontology, protein polypeptide chains, primary metabolites, polypeptide chain, resilient, Roles, DmIKK-gamma, tough, Gene Products, Concepts, Project, tetraoxosulfate(VI), dmIKKgamma, IKK[[gamma]], protein aggregate, Sprains, drug resistance, IKKg, KEY, Key, multicellular organismal biosynthetic process, study, strong, viral infection, single-organism biosynthetic process, nucleotide anabolism, tetrahydrofolate anabolism, skII protein, [SO4](2-), reference sample, formation, anabolism, SULFATE ION, weak, nucleotide formation, E 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Shikimate kinase I, Dmikkgamma, Sulfates, IKK-gamma, response to drug, metabolite, Infection and Infestation, aroK protein, Shikimate kinase II, CG16910, Enterocoque, Sulfuric acid ion(2-), Drug, Protein Gene Products, Gene Proteins, Micrococcus ovalis, DmelCG16910, metabolites, shikimate kinase I, Treatment, virulence, quantitative, skI protein, Strains and Sprains, Proteomes, Sulfate, General activity, presence or absence in organism, sulphate ion"],"name_synonyms":["total expressed protein, Micrococcus ovalis, Enterococcus proteiformis, Micrococcus zymogenes, Biofilm, Streptococcus liquefaciens, Streptococcus glycerinaceus, Enterocoque, Streptococcus Group D, Proteomes., Streptococcus faecalis"],"view_count":["180"],"additional_accession":[]},"is_claimable":true,"name":"Enterococcus faecalis biofilm proteome","description":"The biofilm proteome profile of endodontic and systemic pathogen E. faecalis has been analysed in this study to identify markers associated with its biofilm 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Strong and weak biofilm forming E. faecalis clinical isolates were compared with two standard ATCC strains of E. faecalis in order to elucidate the biological pathways associated with the biofilm formation capability of E. 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