High dynamic range proteome imaging with the structured illumination gel imager
Identifieur interne : 004B74 ( Main/Merge ); précédent : 004B73; suivant : 004B75High dynamic range proteome imaging with the structured illumination gel imager
Auteurs : Phu T. Van [États-Unis] ; Victor Bass [États-Unis] ; Dan Shiwarski [États-Unis] ; Frederick Lanni [États-Unis] ; Jonathan Minden [États-Unis]Source :
- ELECTROPHORESIS [ 0173-0835 ] ; 2014-09.
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.
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DOI: 10.1002/elps.201400126
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xml:lang="en"><term>Electrophoresis, Gel, Two-Dimensional (methods)</term><term>Image Processing, Computer-Assisted</term><term>Lighting</term><term>Limit of Detection</term><term>Proteins (analysis)</term><term>Proteome (analysis)</term><term>Proteomics (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Limite de détection</term><term>Protéines (analyse)</term><term>Protéome (analyse)</term><term>Protéomique ()</term><term>Traitement d'image par ordinateur</term><term>Éclairage</term><term>Électrophorèse bidimensionnelle sur gel ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Proteins</term><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Protéines</term><term>Protéome</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Electrophoresis, Gel, Two-Dimensional</term><term>Proteomics</term></keywords><keywords scheme="MESH" 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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><double doi="10.1002/elps.201400126"><ISTEX><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><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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Van</name><affiliation wicri:level="4"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh</wicri:regionArea><placeName><settlement type="city">Pittsburgh</settlement><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><affiliation wicri:level="4"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh</wicri:regionArea><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Shiwarski, Dan" sort="Shiwarski, Dan" uniqKey="Shiwarski D" first="Dan" last="Shiwarski">Dan Shiwarski</name><affiliation wicri:level="4"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh</wicri:regionArea><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Lanni, Frederick" sort="Lanni, Frederick" uniqKey="Lanni F" first="Frederick" last="Lanni">Frederick Lanni</name><affiliation wicri:level="4"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh</wicri:regionArea><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Minden, Jonathan" sort="Minden, Jonathan" uniqKey="Minden J" first="Jonathan" last="Minden">Jonathan Minden</name><affiliation wicri:level="4"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Carnegie Mellon University, PA, Pittsburgh</wicri:regionArea><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><country xml:lang="fr" wicri:curation="lc">États-Unis</country><wicri:regionArea>: Dr. Jonathan Minden, Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">ELECTROPHORESIS</title><title level="j" type="alt">ELECTROPHORESIS</title><idno type="ISSN">0173-0835</idno><idno type="eISSN">1522-2683</idno><imprint><biblScope unit="vol">35</biblScope><biblScope unit="issue">18</biblScope><biblScope unit="page" from="2642">2642</biblScope><biblScope unit="page" to="2655">2655</biblScope><biblScope unit="page-count">14</biblScope><date type="published" when="2014-09">2014-09</date></imprint><idno type="ISSN">0173-0835</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0173-0835</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="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.</div></front></TEI></ISTEX><PubMed><TEI><teiHeader><fileDesc><titleStmt><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. 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><idno type="wicri:Area/Ncbi/Curation">002572</idno><idno type="wicri:Area/Ncbi/Checkpoint">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. 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></analytic><series><title level="j">Electrophoresis</title><idno type="eISSN">1522-2683</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Electrophoresis, Gel, Two-Dimensional (methods)</term><term>Image Processing, Computer-Assisted</term><term>Lighting</term><term>Limit of Detection</term><term>Proteins (analysis)</term><term>Proteome (analysis)</term><term>Proteomics (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Limite de détection</term><term>Protéines (analyse)</term><term>Protéome (analyse)</term><term>Protéomique ()</term><term>Traitement d'image par ordinateur</term><term>Éclairage</term><term>Électrophorèse bidimensionnelle sur gel ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Proteins</term><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Protéines</term><term>Protéome</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Electrophoresis, Gel, Two-Dimensional</term><term>Proteomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Image Processing, Computer-Assisted</term><term>Lighting</term><term>Limit of Detection</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Limite de détection</term><term>Protéomique</term><term>Traitement d'image par ordinateur</term><term>Éclairage</term><term>Électrophorèse bidimensionnelle sur gel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI></PubMed></double></record>Pour manipuler ce document sous Unix (Dilib)
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