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 : 001962 ( PubMed/Corpus ); précédent : 001961; suivant : 001963A 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 ; Jean-Claude Tabet ; Ivo G. GutSource :
- Rapid communications in mass spectrometry : RCM [ 1097-0231 ] ; 2014.
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
Links to Exploration step
pubmed:24861592Le document en format XML
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<author><name sortKey="Mauger, Florence" sort="Mauger, Florence" uniqKey="Mauger F" first="Florence" last="Mauger">Florence Mauger</name>
<affiliation><nlm:affiliation>CEA/Institut de Génomique/Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057, Evry Cedex, France.</nlm:affiliation>
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<author><name sortKey="Tabet, Jean Claude" sort="Tabet, Jean Claude" uniqKey="Tabet J" first="Jean-Claude" last="Tabet">Jean-Claude Tabet</name>
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<author><name sortKey="Gut, Ivo G" sort="Gut, Ivo G" uniqKey="Gut I" first="Ivo G" last="Gut">Ivo G. Gut</name>
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<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>
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<author><name sortKey="Tabet, Jean Claude" sort="Tabet, Jean Claude" uniqKey="Tabet J" first="Jean-Claude" last="Tabet">Jean-Claude Tabet</name>
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<author><name sortKey="Gut, Ivo G" sort="Gut, Ivo G" uniqKey="Gut I" first="Ivo G" last="Gut">Ivo G. Gut</name>
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<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>
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<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>
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<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term>
<term>Ions</term>
<term>RNA</term>
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<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>
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<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>
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<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24861592</PMID>
<DateCompleted><Year>2015</Year>
<Month>05</Month>
<Day>11</Day>
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<DateRevised><Year>2014</Year>
<Month>05</Month>
<Day>27</Day>
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<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>
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<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>
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<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>
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<ForeName>Florence</ForeName>
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<AffiliationInfo><Affiliation>CEA/Institut de Génomique/Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057, Evry Cedex, France.</Affiliation>
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