Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus.
Identifieur interne : 002577 ( Main/Exploration ); précédent : 002576; suivant : 002578Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus.
Auteurs : Paul Abraham [États-Unis] ; Rachel M. Adams ; Gerald A. Tuskan ; Robert L. HettichSource :
- Journal of proteome research [ 1535-3907 ] ; 2013.
Descripteurs français
- KwdFr :
- Cartographie peptidique (MeSH), Coloration et marquage (méthodes), Génome végétal (MeSH), Méthionine (composition chimique), Oxydoréduction (MeSH), Polymorphisme génétique (MeSH), Populus (composition chimique), Populus (génétique), Protéines végétales (analyse), Protéines végétales (composition chimique), Protéome (analyse), Protéome (composition chimique), Spectrométrie de masse en tandem (MeSH).
- MESH :
- analyse : Protéines végétales, Protéome.
- composition chimique : Méthionine, Populus, Protéines végétales, Protéome.
- génétique : Populus.
- méthodes : Coloration et marquage.
- Cartographie peptidique, Génome végétal, Oxydoréduction, Polymorphisme génétique, Spectrométrie de masse en tandem.
English descriptors
- KwdEn :
- Genome, Plant (MeSH), Methionine (chemistry), Oxidation-Reduction (MeSH), Peptide Mapping (MeSH), Plant Proteins (analysis), Plant Proteins (chemistry), Polymorphism, Genetic (MeSH), Populus (chemistry), Populus (genetics), Proteome (analysis), Proteome (chemistry), Staining and Labeling (methods), Tandem Mass Spectrometry (MeSH).
- MESH :
- chemical , analysis : Plant Proteins, Proteome.
- chemical , chemistry : Methionine, Plant Proteins, Proteome.
- chemistry : Populus.
- genetics : Populus.
- methods : Staining and Labeling.
- Genome, Plant, Oxidation-Reduction, Peptide Mapping, Polymorphism, Genetic, Tandem Mass Spectrometry.
Abstract
The genetic diversity across natural populations of the model organism, Populus, is extensive, containing a single nucleotide polymorphism roughly every 200 base pairs. When deviations from the reference genome occur in coding regions, they can impact protein sequences. Rather than relying on a static reference database to profile protein expression, we employed a peptide sequence tagging (PST) approach capable of decoding the plasticity of the Populus proteome. Using shotgun proteomics data from two genotypes of P. trichocarpa, a tag-based approach enabled the detection of 6653 unexpected sequence variants. Through manual validation, our study investigated how the most abundant chemical modification (methionine oxidation) could masquerade as a sequence variant (Ala→Ser) when few site-determining ions existed. In fact, precise localization of an oxidation site for peptides with more than one potential placement was indeterminate for 70% of the MS/MS spectra. We demonstrate that additional fragment ions made available by high energy collisional dissociation enhances the robustness of the peptide sequence tagging approach (81% of oxidation events could be exclusively localized to a methionine). We are confident that augmenting fragmentation processes for a PST approach will further improve the identification of single amino acid polymorphism in Populus and potentially other species as well.
DOI: 10.1021/pr400192r
PubMed: 23795892
Affiliations:
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Adams</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></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23795892</idno><idno type="pmid">23795892</idno><idno type="doi">10.1021/pr400192r</idno><idno type="wicri:Area/Main/Corpus">002554</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002554</idno><idno type="wicri:Area/Main/Curation">002554</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002554</idno><idno type="wicri:Area/Main/Exploration">002554</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus 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="Adams, Rachel M" sort="Adams, Rachel M" uniqKey="Adams R" first="Rachel M" last="Adams">Rachel M. 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Hettich</name></author></analytic><series><title level="j">Journal of proteome research</title><idno type="eISSN">1535-3907</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genome, Plant (MeSH)</term><term>Methionine (chemistry)</term><term>Oxidation-Reduction (MeSH)</term><term>Peptide Mapping (MeSH)</term><term>Plant Proteins (analysis)</term><term>Plant Proteins (chemistry)</term><term>Polymorphism, Genetic (MeSH)</term><term>Populus (chemistry)</term><term>Populus (genetics)</term><term>Proteome (analysis)</term><term>Proteome (chemistry)</term><term>Staining and Labeling (methods)</term><term>Tandem Mass Spectrometry (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cartographie peptidique (MeSH)</term><term>Coloration et marquage (méthodes)</term><term>Génome végétal (MeSH)</term><term>Méthionine (composition chimique)</term><term>Oxydoréduction (MeSH)</term><term>Polymorphisme génétique (MeSH)</term><term>Populus (composition chimique)</term><term>Populus (génétique)</term><term>Protéines végétales (analyse)</term><term>Protéines végétales (composition chimique)</term><term>Protéome (analyse)</term><term>Protéome (composition chimique)</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" type="chemical" qualifier="chemistry" xml:lang="en"><term>Methionine</term><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="chemistry" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Méthionine</term><term>Populus</term><term>Protéines végétales</term><term>Protéome</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Staining and Labeling</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Coloration et marquage</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Plant</term><term>Oxidation-Reduction</term><term>Peptide Mapping</term><term>Polymorphism, Genetic</term><term>Tandem Mass Spectrometry</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie peptidique</term><term>Génome végétal</term><term>Oxydoréduction</term><term>Polymorphisme génétique</term><term>Spectrométrie de masse en tandem</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The genetic diversity across natural populations of the model organism, Populus, is extensive, containing a single nucleotide polymorphism roughly every 200 base pairs. When deviations from the reference genome occur in coding regions, they can impact protein sequences. Rather than relying on a static reference database to profile protein expression, we employed a peptide sequence tagging (PST) approach capable of decoding the plasticity of the Populus proteome. Using shotgun proteomics data from two genotypes of P. trichocarpa, a tag-based approach enabled the detection of 6653 unexpected sequence variants. Through manual validation, our study investigated how the most abundant chemical modification (methionine oxidation) could masquerade as a sequence variant (Ala→Ser) when few site-determining ions existed. In fact, precise localization of an oxidation site for peptides with more than one potential placement was indeterminate for 70% of the MS/MS spectra. We demonstrate that additional fragment ions made available by high energy collisional dissociation enhances the robustness of the peptide sequence tagging approach (81% of oxidation events could be exclusively localized to a methionine). We are confident that augmenting fragmentation processes for a PST approach will further improve the identification of single amino acid polymorphism in Populus and potentially other species as well. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23795892</PMID><DateCompleted><Year>2014</Year><Month>02</Month><Day>17</Day></DateCompleted><DateRevised><Year>2013</Year><Month>08</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1535-3907</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>8</Issue><PubDate><Year>2013</Year><Month>Aug</Month><Day>02</Day></PubDate></JournalIssue><Title>Journal of proteome research</Title><ISOAbbreviation>J Proteome Res</ISOAbbreviation></Journal><ArticleTitle>Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus.</ArticleTitle><Pagination><MedlinePgn>3642-51</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/pr400192r</ELocationID><Abstract><AbstractText>The genetic diversity across natural populations of the model organism, Populus, is extensive, containing a single nucleotide polymorphism roughly every 200 base pairs. When deviations from the reference genome occur in coding regions, they can impact protein sequences. Rather than relying on a static reference database to profile protein expression, we employed a peptide sequence tagging (PST) approach capable of decoding the plasticity of the Populus proteome. Using shotgun proteomics data from two genotypes of P. trichocarpa, a tag-based approach enabled the detection of 6653 unexpected sequence variants. Through manual validation, our study investigated how the most abundant chemical modification (methionine oxidation) could masquerade as a sequence variant (Ala→Ser) when few site-determining ions existed. In fact, precise localization of an oxidation site for peptides with more than one potential placement was indeterminate for 70% of the MS/MS spectra. We demonstrate that additional fragment ions made available by high energy collisional dissociation enhances the robustness of the peptide sequence tagging approach (81% of oxidation events could be exclusively localized to a methionine). We are confident that augmenting fragmentation processes for a PST approach will further improve the identification of single amino acid polymorphism in Populus and potentially other species as well. </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>Adams</LastName><ForeName>Rachel M</ForeName><Initials>RM</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>2013</Year><Month>07</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Proteome Res</MedlineTA><NlmUniqueID>101128775</NlmUniqueID><ISSNLinking>1535-3893</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical><Chemical><RegistryNumber>AE28F7PNPL</RegistryNumber><NameOfSubstance UI="D008715">Methionine</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008715" MajorTopicYN="N">Methionine</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010084" MajorTopicYN="N">Oxidation-Reduction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010449" MajorTopicYN="N">Peptide Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011110" MajorTopicYN="Y">Polymorphism, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013194" MajorTopicYN="N">Staining and Labeling</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D053719" MajorTopicYN="N">Tandem Mass Spectrometry</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>6</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>6</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>2</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23795892</ArticleId><ArticleId IdType="doi">10.1021/pr400192r</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Adams, Rachel M" sort="Adams, Rachel M" uniqKey="Adams R" first="Rachel M" last="Adams">Rachel M. Adams</name><name sortKey="Hettich, Robert L" sort="Hettich, Robert L" uniqKey="Hettich R" first="Robert L" last="Hettich">Robert L. Hettich</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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