Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus.
Identifieur interne : 002515 ( Main/Exploration ); précédent : 002514; suivant : 002516Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus.
Auteurs : Paul Abraham [États-Unis] ; Richard J. Giannone ; Rachel M. Adams ; Udaya Kalluri ; Gerald A. Tuskan ; Robert L. HettichSource :
- Molecular & cellular proteomics : MCP [ 1535-9484 ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Plant Proteins, Proteome.
- metabolism : Plant Leaves, Plant Proteins, Populus.
- Chromatography, High Pressure Liquid, Protein Processing, Post-Translational, Tandem Mass Spectrometry.
Abstract
High-performance mass spectrometry (MS)-based proteomics enabled the construction of a detailed proteome atlas for Populus, a woody perennial plant model organism. Optimization of experimental procedures and implementation of current state-of-the-art instrumentation afforded the most detailed look into the predicted proteome space of Populus, offering varying proteome perspectives: (1) network-wide, (2) pathway-specific, and (3) protein-level viewpoints. Together, enhanced protein retrieval through a detergent-based lysis approach and maximized peptide sampling via the dual-pressure linear ion trap mass spectrometer (LTQ Velos), have resulted in the identification of 63,056 tryptic peptides. The technological advancements, specifically spectral-acquisition and sequencing speed, afforded the deepest look into the Populus proteome, with peptide abundances spanning 6 orders of magnitude and mapping to ∼25% of the predicted proteome space. In total, tryptic peptides mapped to 11,689 protein assignments across four organ-types: mature (fully expanded, leaf plastichronic index (LPI) 10-12) leaf, young (juvenile, LPI 4-6) leaf, root, and stem. To resolve protein ambiguity, identified proteins were grouped by sequence similarity (≥ 90%), thereby reducing the protein assignments into 7538 protein groups. In addition, this large-scale data set features the first systems-wide survey of protein expression across different Populus organs. As a demonstration of the precision and comprehensiveness of the semiquantitative analysis, we were able to contrast two stages of leaf development, mature versus young leaf. Statistical comparison through ANOVA analysis revealed 1432 protein groups that exhibited statistically significant (p ≤ 0.01) differences in protein abundance. Experimental validation of the metabolic circuitry expected in mature leaf (characterized by photosynthesis and carbon fixation) compared with young leaf (characterized by rapid growth and moderate photosynthetic activities) strongly testifies to the credibility of the approach. Instead of quantitatively comparing a few proteins, a systems view of all the changes associated with a given cellular perturbation could be made.
DOI: 10.1074/mcp.M112.022996
PubMed: 23073815
PubMed Central: PMC3536892
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus.</title><author><name sortKey="Abraham, Paul" sort="Abraham, Paul" uniqKey="Abraham P" first="Paul" last="Abraham">Paul Abraham</name><affiliation wicri:level="1"><nlm:affiliation>Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37830, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37830</wicri:regionArea><wicri:noRegion>Tennessee 37830</wicri:noRegion></affiliation></author><author><name sortKey="Giannone, Richard J" sort="Giannone, Richard J" uniqKey="Giannone R" first="Richard J" last="Giannone">Richard J. 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Giannone</name></author><author><name sortKey="Adams, Rachel M" sort="Adams, Rachel M" uniqKey="Adams R" first="Rachel M" last="Adams">Rachel M. Adams</name></author><author><name sortKey="Kalluri, Udaya" sort="Kalluri, Udaya" uniqKey="Kalluri U" first="Udaya" last="Kalluri">Udaya Kalluri</name></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name></author><author><name sortKey="Hettich, Robert L" sort="Hettich, Robert L" uniqKey="Hettich R" first="Robert L" last="Hettich">Robert L. Hettich</name></author></analytic><series><title level="j">Molecular & cellular proteomics : MCP</title><idno type="eISSN">1535-9484</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromatography, High Pressure Liquid (MeSH)</term><term>Plant Leaves (metabolism)</term><term>Plant Proteins (analysis)</term><term>Plant Proteins (metabolism)</term><term>Populus (metabolism)</term><term>Protein Processing, Post-Translational (MeSH)</term><term>Proteome (analysis)</term><term>Tandem Mass Spectrometry (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chromatographie en phase liquide à haute performance (MeSH)</term><term>Feuilles de plante (métabolisme)</term><term>Maturation post-traductionnelle des protéines (MeSH)</term><term>Populus (métabolisme)</term><term>Protéines végétales (analyse)</term><term>Protéines végétales (métabolisme)</term><term>Protéome (analyse)</term><term>Spectrométrie de masse en tandem (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Plant Proteins</term><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Protéines végétales</term><term>Protéome</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plant Leaves</term><term>Plant Proteins</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Feuilles de plante</term><term>Populus</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromatography, High Pressure Liquid</term><term>Protein Processing, Post-Translational</term><term>Tandem Mass Spectrometry</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Chromatographie en phase liquide à haute performance</term><term>Maturation post-traductionnelle des protéines</term><term>Spectrométrie de masse en tandem</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">High-performance mass spectrometry (MS)-based proteomics enabled the construction of a detailed proteome atlas for Populus, a woody perennial plant model organism. Optimization of experimental procedures and implementation of current state-of-the-art instrumentation afforded the most detailed look into the predicted proteome space of Populus, offering varying proteome perspectives: (1) network-wide, (2) pathway-specific, and (3) protein-level viewpoints. Together, enhanced protein retrieval through a detergent-based lysis approach and maximized peptide sampling via the dual-pressure linear ion trap mass spectrometer (LTQ Velos), have resulted in the identification of 63,056 tryptic peptides. The technological advancements, specifically spectral-acquisition and sequencing speed, afforded the deepest look into the Populus proteome, with peptide abundances spanning 6 orders of magnitude and mapping to ∼25% of the predicted proteome space. In total, tryptic peptides mapped to 11,689 protein assignments across four organ-types: mature (fully expanded, leaf plastichronic index (LPI) 10-12) leaf, young (juvenile, LPI 4-6) leaf, root, and stem. To resolve protein ambiguity, identified proteins were grouped by sequence similarity (≥ 90%), thereby reducing the protein assignments into 7538 protein groups. In addition, this large-scale data set features the first systems-wide survey of protein expression across different Populus organs. As a demonstration of the precision and comprehensiveness of the semiquantitative analysis, we were able to contrast two stages of leaf development, mature versus young leaf. Statistical comparison through ANOVA analysis revealed 1432 protein groups that exhibited statistically significant (p ≤ 0.01) differences in protein abundance. Experimental validation of the metabolic circuitry expected in mature leaf (characterized by photosynthesis and carbon fixation) compared with young leaf (characterized by rapid growth and moderate photosynthetic activities) strongly testifies to the credibility of the approach. Instead of quantitatively comparing a few proteins, a systems view of all the changes associated with a given cellular perturbation could be made.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23073815</PMID><DateCompleted><Year>2013</Year><Month>06</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1535-9484</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>1</Issue><PubDate><Year>2013</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Molecular & cellular proteomics : MCP</Title><ISOAbbreviation>Mol Cell Proteomics</ISOAbbreviation></Journal><ArticleTitle>Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus.</ArticleTitle><Pagination><MedlinePgn>106-19</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1074/mcp.M112.022996</ELocationID><Abstract><AbstractText>High-performance mass spectrometry (MS)-based proteomics enabled the construction of a detailed proteome atlas for Populus, a woody perennial plant model organism. Optimization of experimental procedures and implementation of current state-of-the-art instrumentation afforded the most detailed look into the predicted proteome space of Populus, offering varying proteome perspectives: (1) network-wide, (2) pathway-specific, and (3) protein-level viewpoints. Together, enhanced protein retrieval through a detergent-based lysis approach and maximized peptide sampling via the dual-pressure linear ion trap mass spectrometer (LTQ Velos), have resulted in the identification of 63,056 tryptic peptides. The technological advancements, specifically spectral-acquisition and sequencing speed, afforded the deepest look into the Populus proteome, with peptide abundances spanning 6 orders of magnitude and mapping to ∼25% of the predicted proteome space. In total, tryptic peptides mapped to 11,689 protein assignments across four organ-types: mature (fully expanded, leaf plastichronic index (LPI) 10-12) leaf, young (juvenile, LPI 4-6) leaf, root, and stem. To resolve protein ambiguity, identified proteins were grouped by sequence similarity (≥ 90%), thereby reducing the protein assignments into 7538 protein groups. In addition, this large-scale data set features the first systems-wide survey of protein expression across different Populus organs. As a demonstration of the precision and comprehensiveness of the semiquantitative analysis, we were able to contrast two stages of leaf development, mature versus young leaf. Statistical comparison through ANOVA analysis revealed 1432 protein groups that exhibited statistically significant (p ≤ 0.01) differences in protein abundance. Experimental validation of the metabolic circuitry expected in mature leaf (characterized by photosynthesis and carbon fixation) compared with young leaf (characterized by rapid growth and moderate photosynthetic activities) strongly testifies to the credibility of the approach. Instead of quantitatively comparing a few proteins, a systems view of all the changes associated with a given cellular perturbation could be made.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Abraham</LastName><ForeName>Paul</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37830, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giannone</LastName><ForeName>Richard J</ForeName><Initials>RJ</Initials></Author><Author ValidYN="Y"><LastName>Adams</LastName><ForeName>Rachel M</ForeName><Initials>RM</Initials></Author><Author ValidYN="Y"><LastName>Kalluri</LastName><ForeName>Udaya</ForeName><Initials>U</Initials></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald A</ForeName><Initials>GA</Initials></Author><Author ValidYN="Y"><LastName>Hettich</LastName><ForeName>Robert L</ForeName><Initials>RL</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>2012</Year><Month>10</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Cell Proteomics</MedlineTA><NlmUniqueID>101125647</NlmUniqueID><ISSNLinking>1535-9476</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002851" MajorTopicYN="N">Chromatography, High Pressure 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Adams</name><name sortKey="Giannone, Richard J" sort="Giannone, Richard J" uniqKey="Giannone R" first="Richard J" last="Giannone">Richard J. Giannone</name><name sortKey="Hettich, Robert L" sort="Hettich, Robert L" uniqKey="Hettich R" first="Robert L" last="Hettich">Robert L. Hettich</name><name sortKey="Kalluri, Udaya" sort="Kalluri, Udaya" uniqKey="Kalluri U" first="Udaya" last="Kalluri">Udaya Kalluri</name><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Abraham, Paul" sort="Abraham, Paul" uniqKey="Abraham P" first="Paul" last="Abraham">Paul Abraham</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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