Fast ATOM Bombardment Mass Spectra of Nucleosides. Comparison with Electron Impact and Chemical Ionization Mass Spectra

Slowikowski, Debra L.; Schram, Karl H.

doi:10.1080/07328318508056167

Cited by 30 publications

(9 citation statements)

References 36 publications

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“…The monophosphate anion even shows loss of three waters at m / z 269. This facile loss of water from the molecular ion and various fragment ions is a hallmark of pseudouridine mass spectra, observed even in the absence of collisional activation, by EI, CI, FAB, , and thermospray 17 and electrospray 10 ionization methods.…”

Section: Resultsmentioning

confidence: 99%

Detection of the Common RNA Nucleoside Pseudouridine in Mixtures of Oligonucleotides by Mass Spectrometry

Pomerantz

McCloskey

2005

Anal. Chem.

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Pseudouridine, an isomer of uridine, is probably the most common of many posttranscriptional RNA modifications found in nature. Although mass spectrometry has become widely used in the characterization of modified nucleic acids, its application to the recognition and sequence placement of pseudouridine has not been straightforward, particularly in the case of complex mixtures such as those resulting from selective enzymatic hydrolysis of RNA into oligonucleotides. We report results of a study of the characteristic dissociation reactions of pseudouridine-containing oligonucleotides following ionization by electrospray and use of those pathways in an LC/MS-based method applicable to direct analysis of RNase digests of RNA. As a consequence of the C-C (rather than C-N) glycosidic bond of pseudouridine, the otherwise common dissociation paths involving base loss do not occur, resulting in characteristic formation of a set of low-mass negative ions containing the intact glycosidic bond (m/z 225, 207, 189, 165, 164, 139), which permit recognition of pseudouridine-containing oligonucleotides. Those components can subsequently be subjected to sequence analysis by MS/MS, in which enhancement of selective sequence-determining ions (a-, w-, y-types), and absence of a - base ions, are observed at the site of pseudouridylation. Also, selected reaction pathways can be monitored in the LC/MS/MS analysis that are indicative of pseudouridine at the 5' terminus (m/z 225 --> 165), internal positions (m/z 207 --> 164), and in the RNase T1-derived product Psi pGp (m/z 668 --> 207) arising from the RNA sequence ...G Psi G... These procedures can be effectively integrated into an existing suite of LC/ESI-MS-based methods designed for the analysis of posttranscriptionally modified sites in RNA.

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Section: Resultsmentioning

confidence: 99%

Detection of the Common RNA Nucleoside Pseudouridine in Mixtures of Oligonucleotides by Mass Spectrometry

Pomerantz

McCloskey

2005

Anal. Chem.

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“…MS is significant because tRNA is a heterogeneous mixture, and modified nucleosides only constitute between 0.001% and 0.4% of the total nucleoside content (McCloskey, ). To use MS to analyze modified nucleosides in tRNA, one first needs to consider fragmentation pathways of RNA and nucleosides (Slowikowski & Schram, ). Several factors contribute to RNA fragmentation pathways: The N‐glycosidic bond that joins the ribose and the nucleobase is labile in the same range as the backbone bonds, and loss of a nucleobase channels backbone dissociation into cleavage of the 3′‐proximal C–O bond and c/y ions in RNA fragmentation (Andersen, Kirpekar, & Haselmann, ). The fragmentation pathways are influenced by the analyte, primarily because the stability of the N‐glycosidic bond is nucleobase‐dependent. An increased collision energy produces a more‐diverse fragment ion pattern. The charge state and ion polarity can have a major impact on the dominating fragmentation channels (Giessing & Kirpekar, ).…”

Section: Modified Nucleoside Within Trna Analysismentioning

confidence: 99%

“…MS is significant because tRNA is a heterogeneous mixture, and modified nucleosides only constitute between 0.001% and 0.4% of the total nucleoside content (McCloskey, 1990b). To use MS to analyze modified nucleosides in tRNA, one first needs to consider fragmentation pathways of RNA and nucleosides (Slowikowski & Schram, 1985). Several factors contribute to RNA fragmentation pathways:…”

Section: Modified Nucleoside Within Trna Analysismentioning

confidence: 99%

Mass spectrometry analysis of nucleosides and nucleotides

Dudley

Bond

2013

Mass Spec Rev

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Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.

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“…At the nucleoside level, the N-glycosidic bond is the primary linkage cleaved [58], except for pseudouridine and its derivatives [59], which have C-C glycosidic bonds between ribose and nucleobase. Nucleosides are typically analysed in positive ion mode because of better ion yield, but uridine derivatives may be ionised more efficiently by de-protonation due to their low gas phase proton affinity [60].…”

Section: Rna Fragmentationmentioning

confidence: 99%