High dynamic range proteome imaging with the structured illumination gel imager
Identifieur interne : 002A99 ( Istex/Corpus ); précédent : 002A98; suivant : 002B00High dynamic range proteome imaging with the structured illumination gel imager
Auteurs : Phu T. Van ; Victor Bass ; Dan Shiwarski ; Frederick Lanni ; Jonathan MindenSource :
- ELECTROPHORESIS [ 0173-0835 ] ; 2014-09.
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.
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DOI: 10.1002/elps.201400126
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Van</name><affiliation><mods:affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</mods:affiliation></affiliation></author><author><name sortKey="Bass, Victor" sort="Bass, Victor" uniqKey="Bass V" first="Victor" last="Bass">Victor Bass</name><affiliation><mods:affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</mods:affiliation></affiliation></author><author><name sortKey="Shiwarski, Dan" sort="Shiwarski, Dan" uniqKey="Shiwarski D" first="Dan" last="Shiwarski">Dan Shiwarski</name><affiliation><mods:affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</mods:affiliation></affiliation></author><author><name sortKey="Lanni, Frederick" sort="Lanni, Frederick" uniqKey="Lanni F" first="Frederick" last="Lanni">Frederick Lanni</name><affiliation><mods:affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</mods:affiliation></affiliation></author><author><name sortKey="Minden, Jonathan" sort="Minden, Jonathan" uniqKey="Minden J" first="Jonathan" last="Minden">Jonathan Minden</name><affiliation><mods:affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>: Dr. Jonathan Minden, Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA: : +1‐412‐268‐7129</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: minden@cmu.edu</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:B61C22B8299AF2305BDB0A76DA901A6B27224515</idno><date when="2014" year="2014">2014</date><idno type="doi">10.1002/elps.201400126</idno><idno type="url">https://api.istex.fr/document/B61C22B8299AF2305BDB0A76DA901A6B27224515/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">002A99</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">002A99</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">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><istex><corpusName>wiley</corpusName><author><json:item><name>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.</p></abstract></abstractGroup></contentMeta><noteGroup><note xml:id="elps5197-note-0001" numbered="no"><p><b>Colour Online</b>: See the article online to view Figs. 1, 2,6 and 8 in colour.</p></note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>High dynamic range proteome imaging with the structured illumination gel imager</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Proteomics and 2DE</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>High dynamic range proteome imaging with the structured illumination gel imager</title></titleInfo><name type="personal"><namePart type="given">Phu T.</namePart><namePart type="family">Van</namePart><affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Victor</namePart><namePart type="family">Bass</namePart><affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Dan</namePart><namePart type="family">Shiwarski</namePart><affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Frederick</namePart><namePart type="family">Lanni</namePart><affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jonathan</namePart><namePart type="family">Minden</namePart><affiliation>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh, USA</affiliation><affiliation>: Dr. Jonathan Minden, Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA: : +1‐412‐268‐7129</affiliation><affiliation>E-mail: minden@cmu.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><dateIssued encoding="w3cdtf">2014-09</dateIssued><dateCreated encoding="w3cdtf">2014-06-26</dateCreated><dateCaptured encoding="w3cdtf">2014-03-11</dateCaptured><dateValid encoding="w3cdtf">2014-06-10</dateValid><copyrightDate encoding="w3cdtf">2014</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><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.</abstract><note type="funding">IDBR - No. 1063236; </note><subject><genre>keywords</genre><topic>2DE gels</topic><topic>Fluorescence</topic><topic>Proteomics</topic><topic>Structured illumination</topic></subject><relatedItem type="host"><titleInfo><title>ELECTROPHORESIS</title></titleInfo><titleInfo type="abbreviated"><title>ELECTROPHORESIS</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><subject><genre>article-category</genre><topic>Research Article</topic></subject><identifier type="ISSN">0173-0835</identifier><identifier type="eISSN">1522-2683</identifier><identifier type="DOI">10.1002/(ISSN)1522-2683</identifier><identifier type="PublisherID">ELPS</identifier><part><date>2014</date><detail type="volume"><caption>vol.</caption><number>35</number></detail><detail type="issue"><caption>no.</caption><number>18</number></detail><extent unit="pages"><start>2642</start><end>2655</end><total>14</total></extent></part></relatedItem><identifier type="istex">B61C22B8299AF2305BDB0A76DA901A6B27224515</identifier><identifier type="ark">ark:/67375/WNG-ZVWJ5RGB-F</identifier><identifier type="DOI">10.1002/elps.201400126</identifier><identifier type="ArticleID">ELPS5197</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2014 WILEY‐VCH Verlag GmbH & Co. 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