Ontology type: schema:ScholarlyArticle
2007-02-25
AUTHORSOliver Rinner, Lukas N. Mueller, Martin Hubálek, Markus Müller, Matthias Gstaiger, Ruedi Aebersold
ABSTRACTBiological systems are controlled by protein complexes that associate into dynamic protein interaction networks. We describe a strategy that analyzes protein complexes through the integration of label-free, quantitative mass spectrometry and computational analysis. By evaluating peptide intensity profiles throughout the sequential dilution of samples, the MasterMap system identifies specific interaction partners, detects changes in the composition of protein complexes and reveals variations in the phosphorylation states of components of protein complexes. We use the complexes containing the human forkhead transcription factor FoxO3A to demonstrate the validity and performance of this technology. Our analysis identifies previously known and unknown interactions of FoxO3A with 14-3-3 proteins, in addition to identifying FoxO3A phosphorylation sites and detecting reduced 14-3-3 binding following inhibition of phosphoinositide-3 kinase. By improving specificity and sensitivity of interaction networks, assessing post-translational modifications and providing dynamic interaction profiles, the MasterMap system addresses several limitations of current approaches for protein complexes. More... »
PAGES345-352
http://scigraph.springernature.com/pub.10.1038/nbt1289
DOIhttp://dx.doi.org/10.1038/nbt1289
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1049993666
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/17322870
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biochemistry and Cell Biology",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "14-3-3 Proteins",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Algorithms",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Chromatography, Liquid",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Forkhead Box Protein O3",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Forkhead Transcription Factors",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Internet",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Mass Spectrometry",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Phosphorylation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Protein Interaction Mapping",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Protein Processing, Post-Translational",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Proteome",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Proteomics",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Sensitivity and Specificity",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland",
"id": "http://www.grid.ac/institutes/grid.5801.c",
"name": [
"Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland"
],
"type": "Organization"
},
"familyName": "Rinner",
"givenName": "Oliver",
"id": "sg:person.01055267155.99",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01055267155.99"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland",
"id": "http://www.grid.ac/institutes/grid.5801.c",
"name": [
"Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland"
],
"type": "Organization"
},
"familyName": "Mueller",
"givenName": "Lukas N.",
"id": "sg:person.01253054445.57",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01253054445.57"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, Hradec Kr\u00e1lov\u00e9, Czech Republic",
"id": "http://www.grid.ac/institutes/grid.413094.b",
"name": [
"Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, Hradec Kr\u00e1lov\u00e9, Czech Republic"
],
"type": "Organization"
},
"familyName": "Hub\u00e1lek",
"givenName": "Martin",
"id": "sg:person.0627732620.43",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0627732620.43"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland",
"id": "http://www.grid.ac/institutes/grid.5801.c",
"name": [
"Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland"
],
"type": "Organization"
},
"familyName": "M\u00fcller",
"givenName": "Markus",
"id": "sg:person.0733663303.51",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0733663303.51"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland",
"id": "http://www.grid.ac/institutes/grid.5801.c",
"name": [
"Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland"
],
"type": "Organization"
},
"familyName": "Gstaiger",
"givenName": "Matthias",
"id": "sg:person.015016435467.65",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015016435467.65"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Faculty of Science, University of Zurich, Zurich, Switzerland",
"id": "http://www.grid.ac/institutes/grid.7400.3",
"name": [
"Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland",
"Faculty of Science, University of Zurich, Zurich, Switzerland"
],
"type": "Organization"
},
"familyName": "Aebersold",
"givenName": "Ruedi",
"id": "sg:person.015313356237.76",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015313356237.76"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/415141a",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001484556",
"https://doi.org/10.1038/415141a"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/13690",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029022565",
"https://doi.org/10.1038/13690"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature04670",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033456836",
"https://doi.org/10.1038/nature04670"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature03239",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008948873",
"https://doi.org/10.1038/nature03239"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-0-387-21606-5",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022356842",
"https://doi.org/10.1007/978-0-387-21606-5"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/19328",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009108746",
"https://doi.org/10.1038/19328"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt790",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002942507",
"https://doi.org/10.1038/nbt790"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nsmb713",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031228962",
"https://doi.org/10.1038/nsmb713"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature04532",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043981355",
"https://doi.org/10.1038/nature04532"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature02166",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030347441",
"https://doi.org/10.1038/nature02166"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/415180a",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005267371",
"https://doi.org/10.1038/415180a"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng1101",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002213324",
"https://doi.org/10.1038/ng1101"
],
"type": "CreativeWork"
}
],
"datePublished": "2007-02-25",
"datePublishedReg": "2007-02-25",
"description": "Biological systems are controlled by protein complexes that associate into dynamic protein interaction networks. We describe a strategy that analyzes protein complexes through the integration of label-free, quantitative mass spectrometry and computational analysis. By evaluating peptide intensity profiles throughout the sequential dilution of samples, the MasterMap system identifies specific interaction partners, detects changes in the composition of protein complexes and reveals variations in the phosphorylation states of components of protein complexes. We use the complexes containing the human forkhead transcription factor FoxO3A to demonstrate the validity and performance of this technology. Our analysis identifies previously known and unknown interactions of FoxO3A with 14-3-3 proteins, in addition to identifying FoxO3A phosphorylation sites and detecting reduced 14-3-3 binding following inhibition of phosphoinositide-3 kinase. By improving specificity and sensitivity of interaction networks, assessing post-translational modifications and providing dynamic interaction profiles, the MasterMap system addresses several limitations of current approaches for protein complexes.",
"genre": "article",
"id": "sg:pub.10.1038/nbt1289",
"inLanguage": "en",
"isAccessibleForFree": false,
"isFundedItemOf": [
{
"id": "sg:grant.2431409",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1115214",
"issn": [
"1087-0156",
"1546-1696"
],
"name": "Nature Biotechnology",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "3",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "25"
}
],
"keywords": [
"protein complexes",
"protein interaction networks",
"interaction networks",
"dynamic protein interaction networks",
"Forkhead transcription factor FOXO3a",
"quantitative mass spectrometry",
"specific interaction partners",
"post-translational modifications",
"transcription factor FOXO3a",
"phosphoinositide-3 kinase",
"phosphorylation sites",
"phosphorylation state",
"interaction partners",
"mass spectrometry",
"unknown interactions",
"complexes",
"biological systems",
"FOXO3a",
"interaction profiles",
"computational analysis",
"sequential dilution",
"kinase",
"spectrometry",
"protein",
"integrated mass",
"binding",
"computational framework",
"inhibition",
"sites",
"specificity",
"modification",
"composition",
"analysis",
"interaction",
"profile",
"dilution",
"variation",
"partners",
"current approaches",
"samples",
"components",
"system",
"changes",
"addition",
"intensity profiles",
"sensitivity",
"network",
"state",
"mass",
"strategies",
"performance",
"limitations",
"technology",
"integration",
"approach",
"framework",
"validity"
],
"name": "An integrated mass spectrometric and computational framework for the analysis of protein interaction networks",
"pagination": "345-352",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1049993666"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/nbt1289"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"17322870"
]
}
],
"sameAs": [
"https://doi.org/10.1038/nbt1289",
"https://app.dimensions.ai/details/publication/pub.1049993666"
],
"sdDataset": "articles",
"sdDatePublished": "2022-05-20T07:24",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220519/entities/gbq_results/article/article_446.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1038/nbt1289"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nbt1289'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nbt1289'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt1289'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nbt1289'
This table displays all metadata directly associated to this object as RDF triples.
263 TRIPLES
22 PREDICATES
108 URIs
88 LITERALS
20 BLANK NODES