High dynamic range proteome imaging with the structured illumination gel imager.
Identifieur interne : 002572 ( Ncbi/Merge ); précédent : 002571; suivant : 002573High dynamic range proteome imaging with the structured illumination gel imager.
Auteurs : Phu T. Van [États-Unis] ; Victor Bass ; Dan Shiwarski ; Frederick Lanni ; Jonathan MindenSource :
- Electrophoresis [ 1522-2683 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Proteins, Proteome.
- methods : Electrophoresis, Gel, Two-Dimensional, Proteomics.
- Image Processing, Computer-Assisted, Lighting, Limit of Detection.
Abstract
A current challenge for proteomics is detecting proteins over the large concentration ranges found in complex biological samples such as whole-cell extracts. Currently, no unbiased, whole-proteome analysis scheme is capable of detecting the full range of cellular proteins. This is due in part to the limited dynamic range of the detectors used to sense proteins or peptides. We present a new technology, structured illumination (SI) gel imager, which detects fluorescently labeled proteins in electrophoretic gels over a 1 000 000-fold concentration range. SI uses computer-generated masks to attenuate the illumination of highly abundant proteins, allowing for long exposures of low-abundance proteins, thus avoiding detector saturation. A series of progressively masked gel images are assembled into a single, very high dynamic range image. We demonstrate that the SI imager can detect proteins over a concentration range of approximately 1 000 000-fold, making it a useful tool for comprehensive, unbiased proteome-wide surveys.
DOI: 10.1002/elps.201400126
PubMed: 24935033
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Van</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Bass, Victor" sort="Bass, Victor" uniqKey="Bass V" first="Victor" last="Bass">Victor Bass</name></author><author><name sortKey="Shiwarski, Dan" sort="Shiwarski, Dan" uniqKey="Shiwarski D" first="Dan" last="Shiwarski">Dan Shiwarski</name></author><author><name sortKey="Lanni, Frederick" sort="Lanni, Frederick" uniqKey="Lanni F" first="Frederick" last="Lanni">Frederick Lanni</name></author><author><name sortKey="Minden, Jonathan" sort="Minden, Jonathan" uniqKey="Minden J" first="Jonathan" last="Minden">Jonathan Minden</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24935033</idno><idno type="pmid">24935033</idno><idno type="doi">10.1002/elps.201400126</idno><idno type="wicri:Area/PubMed/Corpus">001B83</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001B83</idno><idno type="wicri:Area/PubMed/Curation">001B75</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001B75</idno><idno type="wicri:Area/PubMed/Checkpoint">001B75</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001B75</idno><idno type="wicri:Area/Ncbi/Merge">002572</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">High dynamic range proteome imaging with the structured illumination gel imager.</title><author><name sortKey="Van, Phu T" sort="Van, Phu T" uniqKey="Van P" first="Phu T" last="Van">Phu T. 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Currently, no unbiased, whole-proteome analysis scheme is capable of detecting the full range of cellular proteins. This is due in part to the limited dynamic range of the detectors used to sense proteins or peptides. We present a new technology, structured illumination (SI) gel imager, which detects fluorescently labeled proteins in electrophoretic gels over a 1 000 000-fold concentration range. SI uses computer-generated masks to attenuate the illumination of highly abundant proteins, allowing for long exposures of low-abundance proteins, thus avoiding detector saturation. A series of progressively masked gel images are assembled into a single, very high dynamic range image. We demonstrate that the SI imager can detect proteins over a concentration range of approximately 1 000 000-fold, making it a useful tool for comprehensive, unbiased proteome-wide surveys.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24935033</PMID><DateCreated><Year>2014</Year><Month>09</Month><Day>08</Day></DateCreated><DateCompleted><Year>2015</Year><Month>05</Month><Day>12</Day></DateCompleted><DateRevised><Year>2014</Year><Month>09</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1522-2683</ISSN><JournalIssue CitedMedium="Internet"><Volume>35</Volume><Issue>18</Issue><PubDate><Year>2014</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Electrophoresis</Title><ISOAbbreviation>Electrophoresis</ISOAbbreviation></Journal><ArticleTitle>High dynamic range proteome imaging with the structured illumination gel imager.</ArticleTitle><Pagination><MedlinePgn>2642-55</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/elps.201400126</ELocationID><Abstract><AbstractText>A current challenge for proteomics is detecting proteins over the large concentration ranges found in complex biological samples such as whole-cell extracts. Currently, no unbiased, whole-proteome analysis scheme is capable of detecting the full range of cellular proteins. This is due in part to the limited dynamic range of the detectors used to sense proteins or peptides. We present a new technology, structured illumination (SI) gel imager, which detects fluorescently labeled proteins in electrophoretic gels over a 1 000 000-fold concentration range. SI uses computer-generated masks to attenuate the illumination of highly abundant proteins, allowing for long exposures of low-abundance proteins, thus avoiding detector saturation. A series of progressively masked gel images are assembled into a single, very high dynamic range image. We demonstrate that the SI imager can detect proteins over a concentration range of approximately 1 000 000-fold, making it a useful tool for comprehensive, unbiased proteome-wide surveys.</AbstractText><CopyrightInformation>© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Van</LastName><ForeName>Phu T</ForeName><Initials>PT</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bass</LastName><ForeName>Victor</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Shiwarski</LastName><ForeName>Dan</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Lanni</LastName><ForeName>Frederick</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Minden</LastName><ForeName>Jonathan</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>08</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Electrophoresis</MedlineTA><NlmUniqueID>8204476</NlmUniqueID><ISSNLinking>0173-0835</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011506">Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D015180" MajorTopicYN="N">Electrophoresis, Gel, Two-Dimensional</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007091" MajorTopicYN="N">Image Processing, Computer-Assisted</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008029" MajorTopicYN="Y">Lighting</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D057230" MajorTopicYN="N">Limit of Detection</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011506" MajorTopicYN="N">Proteins</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D040901" MajorTopicYN="N">Proteomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">2DE gels</Keyword><Keyword MajorTopicYN="N">Fluorescence</Keyword><Keyword MajorTopicYN="N">Proteomics</Keyword><Keyword MajorTopicYN="N">Structured illumination</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>03</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2014</Year><Month>05</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>06</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>6</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>6</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>5</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24935033</ArticleId><ArticleId IdType="doi">10.1002/elps.201400126</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li></region><settlement><li>Pittsburgh</li></settlement><orgName><li>Université Carnegie-Mellon</li></orgName></list><tree><noCountry><name sortKey="Bass, Victor" sort="Bass, Victor" uniqKey="Bass V" first="Victor" last="Bass">Victor Bass</name><name sortKey="Lanni, Frederick" sort="Lanni, Frederick" uniqKey="Lanni F" first="Frederick" last="Lanni">Frederick Lanni</name><name sortKey="Minden, Jonathan" sort="Minden, Jonathan" uniqKey="Minden J" first="Jonathan" last="Minden">Jonathan Minden</name><name sortKey="Shiwarski, Dan" sort="Shiwarski, Dan" uniqKey="Shiwarski D" first="Dan" last="Shiwarski">Dan Shiwarski</name></noCountry><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Van, Phu T" sort="Van, Phu T" uniqKey="Van P" first="Phu T" last="Van">Phu T. 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