Study of the mass spectrometric fragmentation of pseudouridine: comparison of fragmentation data obtained by matrix‐assisted laser desorption/ionisation post‐source decay, electrospray ion trap multistage mass spectrometry, and by a method utilising electrospray quadrupole time‐of‐flight tandem mass spectrometry and in‐source fragmentation

Dudley, Edward G.; Tuytten, Robin; Bond, A. Elizabeth; Lemière, Filip; Brenton, A.G.; Esmans, Eddy L.; Newton, Russell P.

doi:10.1002/rcm.2151

Cited by 41 publications

(39 citation statements)

References 29 publications

(45 reference statements)

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“…The further eliminations of H 2 O and NH 3 ϩ· ), with the latter being the most abundant. From these two product ions multiple losses of HCN and/or CO showed, as commonly seen in the dissociation pathways of nucleosides [5,6,9,15,16]. It has to be noted that once more an addition of H 2 O in the collision cell was observed; the radical ion at m/z 109 formed an adduct with H 2 O yielding the radical ion at m/z 127 (C 4 …”

Section: : a Results Of Ch 3 Oh-adduct Formation And Ch 3 Oh-gas-phasementioning

confidence: 84%

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In-source CID of guanosine: Gas phase ion-molecule reactions

Tuytten

Lemière

Esmans

et al. 2006

J. Am. Soc. Mass Spectrom.

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In-source collision induced dissociation was applied to access second generation ions of protonated guanosine. The in-source gas-phase behavior of [BH 2 ] ϩ -NH 3 (m/z 135, C 5 H 3 N 4 O ϩ ) was investigated. Adduct formation and reactions with available solvent molecules (H 2 O and CH 3 OH) were demonstrated. Several addition/elimination sequences were observed for this particular ion and solvent molecules. Dissociation pathways for the newly formed ions were developed using a QqTOF mass spectrometer, permitting the assignment of elemental compositions of all product ions produced. Reaction schemes were suggested arising from the ring-opened intermediate of the protonated base moiety [BH 2 ] ϩ , obtained from fragmentation of guanosine. The mass spectral data revealed that the in-source CH 3 OH-reaction product underwent more complex fragmentations than the comparable ion following reaction with H 2 O. A rearrangement and a parallel radical dissociation pathway were discerned. Apart from the mass spectrometric evidence, the fragmentation schemes are supported by density functional theory calculations, in which the reaction of the ring-opened protonated guanine intermediate with CH 3 OH and a number of subsequent fragmentations were elaborated. uring the last decade, most fragmentation pathways were elaborated on triple quadrupole (QqQ) and particularly quadrupole ion-trap (QIT) instruments. The latter's capabilities of accessing MS n product ions by applying repeated stages of mass selection and fragmentation proved to be very useful [1]. The maturation of the time of flight (TOF) technology and, more importantly, its use in hybrid-arrangements such as the popular orthogonal QqTOF mass spectrometer made accurate mass data of product ions more readily available [2]. In many cases, the elemental compositions of the product ions can unambiguously be assigned when using a QqTOF mass spectrometer. Product ions lower in the genealogical ladder are also accessible by applying relatively high collision energies in the collision cell. Yet disentanglement of different dissociation pathways originating from a communal progenitor is -in general-still confined to QIT set ups, although the interpretation of energy resolved spectra also has proven its usefulness [3].Recently we and others showed [4 -6] that by making optimal use of in-source CID, combined with the inherent tandem MS capabilities of the QqTOF, what is in effect up to MS 5 data can be acquired. Compared to QIT data the QqTOF data obtained is superior in respect of higher mass accuracy. On the other hand QIT-CID experiments, in general, access almost exclusively the dissociation reaction channels of the lowest energy of activation [7]. This energy-dependent information can

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Section: : a Results Of Ch 3 Oh-adduct Formation And Ch 3 Oh-gas-phasementioning

confidence: 84%

“…This energy-dependent information can pass unrecognized in QqTOF tandem MS experiments due to a less controlled energy deposit on the parent ions. However, in QqTOF experiments fragmentation pathways with higher activation energies become within reach due to higher energy-transfer in a single collision at high CE settings [6,7].…”

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confidence: 99%

In-source CID of guanosine: Gas phase ion-molecule reactions

Tuytten

Lemière

Esmans

et al. 2006

J. Am. Soc. Mass Spectrom.

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“…Quadrupole time-of-flight (QTOF) mass spectrometry was reported to be able to produce valuable MS 3 and MS 4 data in addition to the usual MS/MS data, 15 which is generally only obtained by ion trap and Fourier transform ion cyclotron resonance mass spectrometers. By making optimal use of in-source CID, product ions of the initial precursor ion can first be formed in the ESI source; hence MS/MS and even higher MS n product ions become available for further fragmentation in the collision cell of the QTOF mass spectrometer.…”

Section: Accurate Mass In Characterisation Of Fragmentationmentioning

confidence: 99%

Mass spectrometry analysis of terpene lactones in Ginkgo biloba

Ding

Dudley

Song

et al. 2008

Rapid Comm Mass Spectrometry

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Terpene lactones are a family of compounds with unique chemical structures, first recognised in an extract of Ginkgo biloba. The discovery of terpene lactone derivatives has recently been reported in more and more plant extracts and even food products. In this study, mass spectrometric characteristics of the standard terpene lactones in Ginkgo biloba were comprehensively studied using both an ion trap and a quadrupole time-of-flight (QTOF) mass spectrometer. The mass spectral fragmentation data from both techniques was compared to obtain the mass spectrometric fragmentation pathways of the terpene lactones with high confidence. The data obtained will facilitate the analysis and identification of terpene lactones in future plant research via the fragmentation knowledge reported here.

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“…2B). In addition, lack of neutral loss serves as a distinguishing feature to discriminate pseudouridine (Ψ) from uridine (Dudley et al 2005). To compare the relative change in tRNA modification levels as a function of temperature, we adapted pyQms in a newly developed pipeline system for the analysis of nucleoside modifications.…”

Section: Mass Spectrometry Analysis Of Trna Modification Levels Reveamentioning

confidence: 99%

An evolutionary approach uncovers a diverse response of tRNA 2-thiolation to elevated temperatures in yeast

Alings

Sarin

Fufezan

et al. 2014

RNA

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Chemical modifications of transfer RNA (tRNA) molecules are evolutionarily well conserved and critical for translation and tRNA structure. Little is known how these nucleoside modifications respond to physiological stress. Using mass spectrometry and complementary methods, we defined tRNA modification levels in six yeast species in response to elevated temperatures. We show that 2-thiolation of uridine at position 34 (s 2 U 34 ) is impaired at temperatures exceeding 30°C in the commonly used Saccharomyces cerevisiae laboratory strains S288C and W303, and in Saccharomyces bayanus. Upon stress relief, thiolation levels recover and we find no evidence that modified tRNA or s 2 U 34 nucleosides are actively removed. Our results suggest that loss of 2-thiolation follows accumulation of newly synthesized tRNA that lack s 2 U 34 modification due to temperature sensitivity of the URM1 pathway in S. cerevisiae and S. bayanus. Furthermore, our analysis of the tRNA modification pattern in selected yeast species revealed two alternative phenotypes. Most strains moderately increase their tRNA modification levels in response to heat, possibly constituting a common adaptation to high temperatures. However, an overall reduction of nucleoside modifications was observed exclusively in S288C. This surprising finding emphasizes the importance of studies that utilize the power of evolutionary biology, and highlights the need for future systematic studies on tRNA modifications in additional model organisms.

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Cited by 41 publications

References 29 publications

In-source CID of guanosine: Gas phase ion-molecule reactions

In-source CID of guanosine: Gas phase ion-molecule reactions

Mass spectrometry analysis of terpene lactones in Ginkgo biloba

An evolutionary approach uncovers a diverse response of tRNA 2-thiolation to elevated temperatures in yeast

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