Modified Quadrupole Ion Trap Mass Spectrometer for Infrared Ion Spectroscopy: Application to Protonated Thiated Uridines

Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon d...

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Published inJournal of the American Society for Mass Spectrometry Vol. 29; no. 11; pp. 2125 - 2137
Main Authors Hamlow, L. A., Zhu, Y., Devereaux, Zachary J., Cunningham, N. A., Berden, G., Oomens, J., Rodgers, M. T.
Format Journal Article
LanguageEnglish
Published New York Springer US 01.11.2018
Springer Nature B.V
Subjects
Analytical Chemistry
ATOMIC AND MOLECULAR PHYSICS
Bioinformatics
Biotechnology
Chemistry
Chemistry and Materials Science
COMPARATIVE EVALUATIONS
INFRARED SPECTRA
Infrared spectrometers
Infrared spectroscopy
INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY
ION SPECTROSCOPY
Ions
MASS SPECTROMETERS
Mass spectrometry
Optical Parametric Oscillators
Organic Chemistry
Parametric amplifiers
PARAMETRIC OSCILLATORS
Proteomics
Protonation
QUADRUPOLES
Research Article
Spectra
Spectrum analysis
TRAPS
4-Thiouridine
IRMPD
Infrared multiple photon dissociation action spectroscopy
Uridine
QIT MS
2-Thiouridine
RNA modifications
Quadrupole ion trap mass spectrometer
Online AccessGet full text

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Abstract Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s 2 Urd+H] + , and 4-thiouridine, [s 4 Urd+H] + . The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2′- endo and C3′- endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine. Graphical Abstract ᅟ
AbstractList Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s{sup 2}Urd+H]{sup +}, and 4-thiouridine, [s{sup 4}Urd+H]{sup +}. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2′-endo and C3′-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine. .
Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s 2 Urd+H] + , and 4-thiouridine, [s 4 Urd+H] + . The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2′- endo and C3′- endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine. Graphical Abstract ᅟ
Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s Urd+H] , and 4-thiouridine, [s Urd+H] . The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2'-endo and C3'-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine. Graphical Abstract ᅟ.
Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s2Urd+H]+, and 4-thiouridine, [s4Urd+H]+. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2′-endo and C3′-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine.
Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s2Urd+H]+, and 4-thiouridine, [s4Urd+H]+. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2'-endo and C3'-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine. Graphical Abstract ᅟ.
Author Devereaux, Zachary J.
Rodgers, M. T.
Hamlow, L. A.
Cunningham, N. A.
Berden, G.
Oomens, J.
Zhu, Y.
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  email: mrodgers@chem.wayne.edu
  organization: Department of Chemistry, Wayne State University
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Keywords 4-Thiouridine
IRMPD
Infrared multiple photon dissociation action spectroscopy
Uridine
QIT MS
2-Thiouridine
RNA modifications
Quadrupole ion trap mass spectrometer
Language English
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Snippet Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for...
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SubjectTerms Analytical Chemistry
ATOMIC AND MOLECULAR PHYSICS
Bioinformatics
Biotechnology
Chemistry
Chemistry and Materials Science
COMPARATIVE EVALUATIONS
INFRARED SPECTRA
Infrared spectrometers
Infrared spectroscopy
INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY
ION SPECTROSCOPY
Ions
MASS SPECTROMETERS
Mass spectrometry
Optical Parametric Oscillators
Organic Chemistry
Parametric amplifiers
PARAMETRIC OSCILLATORS
Proteomics
Protonation
QUADRUPOLES
Research Article
Spectra
Spectrum analysis
TRAPS
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Title Modified Quadrupole Ion Trap Mass Spectrometer for Infrared Ion Spectroscopy: Application to Protonated Thiated Uridines
URI https://link.springer.com/article/10.1007/s13361-018-2047-2
https://www.ncbi.nlm.nih.gov/pubmed/30136214
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https://www.osti.gov/biblio/22776793
Volume 29
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