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

• Published in: Journal 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
• Language: English
• 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
• ISSN: 1044-0305; 1879-1123
• DOI: 10.1007/s13361-018-2047-2

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