A revisit of high collision energy effects on collision-induced dissociation spectra using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-LIFT-TOF/TOF): application to the sequencing of RNA/DNA chimeras.
Identifieur interne : 001A12 ( PubMed/Checkpoint ); précédent : 001A11; suivant : 001A13A revisit of high collision energy effects on collision-induced dissociation spectra using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-LIFT-TOF/TOF): application to the sequencing of RNA/DNA chimeras.
Auteurs : Florence Mauger [France] ; Jean-Claude Tabet ; Ivo G. GutSource :
- Rapid communications in mass spectrometry : RCM [ 1097-0231 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Ions, RNA.
- methods : Sequence Analysis, DNA, Sequence Analysis, RNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization.
Abstract
High-energy collision-induced dissociation (CID) spectra of isomeric RNA/DNA chimeras using matrix-assisted laser desorption/ionization time-of-flight LIFT mass spectrometry (MALDI-LIFT-TOF/TOF) can potentially be applied for an exhaustive fragment characterization in a nucleic acid sequencing scheme. These chimeras contain deoxynucleotides and at the 3'-end a ribonucleotide with a 3'-phosphate group.
DOI: 10.1002/rcm.6913
PubMed: 24861592
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A revisit of high collision energy effects on collision-induced dissociation spectra using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-LIFT-TOF/TOF): application to the sequencing of RNA/DNA chimeras.</title><author><name sortKey="Mauger, Florence" sort="Mauger, Florence" uniqKey="Mauger F" first="Florence" last="Mauger">Florence Mauger</name><affiliation wicri:level="3"><nlm:affiliation>CEA/Institut de Génomique/Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057, Evry Cedex, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CEA/Institut de Génomique/Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057, Evry Cedex</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Tabet, Jean Claude" sort="Tabet, Jean Claude" uniqKey="Tabet J" first="Jean-Claude" last="Tabet">Jean-Claude Tabet</name></author><author><name sortKey="Gut, Ivo G" sort="Gut, Ivo G" uniqKey="Gut I" first="Ivo G" last="Gut">Ivo G. Gut</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24861592</idno><idno type="pmid">24861592</idno><idno type="doi">10.1002/rcm.6913</idno><idno type="wicri:Area/PubMed/Corpus">001962</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001962</idno><idno type="wicri:Area/PubMed/Curation">001962</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001962</idno><idno type="wicri:Area/PubMed/Checkpoint">001A12</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001A12</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A revisit of high collision energy effects on collision-induced dissociation spectra using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-LIFT-TOF/TOF): application to the sequencing of RNA/DNA chimeras.</title><author><name sortKey="Mauger, Florence" sort="Mauger, Florence" uniqKey="Mauger F" first="Florence" last="Mauger">Florence Mauger</name><affiliation wicri:level="3"><nlm:affiliation>CEA/Institut de Génomique/Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057, Evry Cedex, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CEA/Institut de Génomique/Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057, Evry Cedex</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Tabet, Jean Claude" sort="Tabet, Jean Claude" uniqKey="Tabet J" first="Jean-Claude" last="Tabet">Jean-Claude Tabet</name></author><author><name sortKey="Gut, Ivo G" sort="Gut, Ivo G" uniqKey="Gut I" first="Ivo G" last="Gut">Ivo G. Gut</name></author></analytic><series><title level="j">Rapid communications in mass spectrometry : RCM</title><idno type="eISSN">1097-0231</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA (chemistry)</term><term>Ions (chemistry)</term><term>RNA (chemistry)</term><term>Sequence Analysis, DNA (methods)</term><term>Sequence Analysis, RNA (methods)</term><term>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ARN ()</term><term>Analyse de séquence d'ADN ()</term><term>Analyse de séquence d'ARN ()</term><term>Ions ()</term><term>Spectrométrie de masse MALDI ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Ions</term><term>RNA</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term><term>Sequence Analysis, RNA</term><term>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>ARN</term><term>Analyse de séquence d'ADN</term><term>Analyse de séquence d'ARN</term><term>Ions</term><term>Spectrométrie de masse MALDI</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">High-energy collision-induced dissociation (CID) spectra of isomeric RNA/DNA chimeras using matrix-assisted laser desorption/ionization time-of-flight LIFT mass spectrometry (MALDI-LIFT-TOF/TOF) can potentially be applied for an exhaustive fragment characterization in a nucleic acid sequencing scheme. These chimeras contain deoxynucleotides and at the 3'-end a ribonucleotide with a 3'-phosphate group.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24861592</PMID><DateCompleted><Year>2015</Year><Month>05</Month><Day>11</Day></DateCompleted><DateRevised><Year>2014</Year><Month>05</Month><Day>27</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1097-0231</ISSN><JournalIssue CitedMedium="Internet"><Volume>28</Volume><Issue>13</Issue><PubDate><Year>2014</Year><Month>Jul</Month><Day>15</Day></PubDate></JournalIssue><Title>Rapid communications in mass spectrometry : RCM</Title><ISOAbbreviation>Rapid Commun. Mass Spectrom.</ISOAbbreviation></Journal><ArticleTitle>A revisit of high collision energy effects on collision-induced dissociation spectra using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-LIFT-TOF/TOF): application to the sequencing of RNA/DNA chimeras.</ArticleTitle><Pagination><MedlinePgn>1433-43</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/rcm.6913</ELocationID><Abstract><AbstractText Label="RATIONALE" NlmCategory="BACKGROUND">High-energy collision-induced dissociation (CID) spectra of isomeric RNA/DNA chimeras using matrix-assisted laser desorption/ionization time-of-flight LIFT mass spectrometry (MALDI-LIFT-TOF/TOF) can potentially be applied for an exhaustive fragment characterization in a nucleic acid sequencing scheme. These chimeras contain deoxynucleotides and at the 3'-end a ribonucleotide with a 3'-phosphate group.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">Deprotonated RNA/DNA chimeras of 4-, 5-, 7- and 10-mers are analyzed by CID. This enhances consecutive dissociations from both the precursor and prompt product anions generated by MALDI and metastable fragmentations prior to entering the LIFT cell.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Gas-phase fragmentations of 4- and 5-mers produced many fragment ions, from base release prior to consecutive cleavage of the nucleotide phosphate bond linkage phosphate. The unusual a4(-) product ion is a specific and diagnostic dissociation of the 4-mer if the ribonucleotide contains cytosine. As the size of RNA/DNA chimeras increase, several abundant product ions are generated mainly from zwitterionic forms (deprotonated phosphate ester and protonated base sites): [(M-H)-BiH](-), [ai-BiH](-), wj(-), [wj, (ai-BiH)](-) (if Bi ≠ T) as internal product ion, and more rarely [wj-BiH](-). The absence of the majority of the [ai-BiH](-) series although the wj (-) series suggested that the higher critical energy processes with a loose transition state are favored yielding the wj(-) series. A large number of abundant fragment ions are detected which enable each isomer to be sequenced.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This sequencing method is high-throughput, accurate and could be used to sequence isomers of up to 10-mers and also oligonucleotides of unknown sequence. However, RNA/DNA chimeras without thymine must be sufficiently concentrated to reach desorption of deprotonated molecular species to be selected in LIFT to produce all fragment ions within measurable abundances.</AbstractText><CopyrightInformation>Copyright © 2014 John Wiley & Sons, Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mauger</LastName><ForeName>Florence</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>CEA/Institut de Génomique/Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057, Evry Cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tabet</LastName><ForeName>Jean-Claude</ForeName><Initials>JC</Initials></Author><Author ValidYN="Y"><LastName>Gut</LastName><ForeName>Ivo G</ForeName><Initials>IG</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Rapid Commun Mass Spectrom</MedlineTA><NlmUniqueID>8802365</NlmUniqueID><ISSNLinking>0951-4198</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D007477">Ions</NameOfSubstance></Chemical><Chemical><RegistryNumber>63231-63-0</RegistryNumber><NameOfSubstance UI="D012313">RNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007477" MajorTopicYN="N">Ions</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012313" MajorTopicYN="N">RNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019032" MajorTopicYN="N">Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>12</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2014</Year><Month>04</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>04</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>5</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>5</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>5</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24861592</ArticleId><ArticleId IdType="doi">10.1002/rcm.6913</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Île-de-France</li></region><settlement><li>Évry (Essonne)</li></settlement></list><tree><noCountry><name sortKey="Gut, Ivo G" sort="Gut, Ivo G" uniqKey="Gut I" first="Ivo G" last="Gut">Ivo G. Gut</name><name sortKey="Tabet, Jean Claude" sort="Tabet, Jean Claude" uniqKey="Tabet J" first="Jean-Claude" last="Tabet">Jean-Claude Tabet</name></noCountry><country name="France"><region name="Île-de-France"><name sortKey="Mauger, Florence" sort="Mauger, Florence" uniqKey="Mauger F" first="Florence" last="Mauger">Florence Mauger</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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