Comparison of negative and positive ion electrospray tandem mass spectrometry for the liquid chromatography tandem mass spectrometry analysis of oxidized deoxynucleosides

Hua, Yousheng; Wainhaus, Samuel B.; Yang, Yanan; Shen, Lixin; Xiong, Yansan; Xu, Xiao‐Ying; Zhang, Fagen; Bolton, Judy L.; Breemen, Richard B. van

doi:10.1016/s1044-0305(00)00191-4

Cited by 84 publications

(68 citation statements)

References 25 publications

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“…The consecutive neutral losses of an HNCO moiety and a C 3 H 6 O 3 fragment has been observed previously upon the collisional activation of the [M Ϫ H] Ϫ ion of 5-hydroxymethyl-2 = -deoxyuridine [18]. In addition, the neutral loss of [19], and pyrimidine glycols [20].…”

Section: Resultssupporting

confidence: 56%

Differentiation of 2′-O- and 3′-O-methylated Ribonucleosides by tandem mass spectrometry

Zhang

Wang

2006

J. Am. Soc. Mass Spectrom.

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Recent studies revealed that the 3=-terminal nucleotides in plant microRNAs were methylated on the ribose at the 2= or 3= hydroxyl groups. Here we examined the fragmentation of the electrospray-produced [M ϩ H] ϩ and [M Ϫ H] Ϫ ions of 2=-and 3=-O-methylated ribonucleosides. It turned out that the predominant fragmentation pathway for the [M ϩ H] ϩ ions of ribose-methylated nucleosides was the neutral loss of the methylated ribose, which made it impossible to distinguish 2=-O-methylation from 3=-O-methylation by positive-ion MS/MS. However, characteristic fragment ions, resulting from the cleavage through the ribose rings, were produced for the [M Ϫ H] Ϫ ions of each pair of ribose-methylated nucleosides. In this respect, the neutral loss of a 90-Da fragment (C 3 H 6 O 3 ) was observed for 2=-O-methylated cytidine, guanosine and adenosine, but not for their 3=-O-methylated counterparts. On the other hand, the neutral loss of a 60-Da fragment (C 2 H 4 O 2 ) was found for 3=-O-methyluridine, but not for 2=-O-methyluridine.

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Section: Resultssupporting

confidence: 56%

Differentiation of 2′-O- and 3′-O-methylated Ribonucleosides by tandem mass spectrometry

Zhang

Wang

2006

J. Am. Soc. Mass Spectrom.

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“…For quantification, we isolated a stable isotope-labeled analog of 8-OH-dAdo in pure form for the first time and used it as the internal standard. It should be pointed out that the use of liquid chromatography/tandem mass spectrometry (LC/MS/MS) has also been reported for the identification of 8-OH-dAdo (45)(46)(47)(48). However, the isotope-dilution technique has been applied for quantification in two instances only (45,48).…”

Section: Fig 2 Structure Of Csb and The Location Of Designed Mutantsmentioning

confidence: 99%

The Cockayne Syndrome Group B Gene Product Is Involved in Cellular Repair of 8-Hydroxyadenine in DNA

Tuo¹,

Jaruga²,

Rodriguez³

et al. 2002

Journal of Biological Chemistry

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Cockayne syndrome (CS) is a human disease characterized by sensitivity to sunlight, severe neurological abnormalities, and accelerated aging. CS has two complementation groups, CS-A and CS-B. The CSB gene encodes the CSB protein with 1493 amino acids. We previously reported that the CSB protein is involved in cellular repair of 8-hydroxyguanine, an abundant lesion in oxidatively damaged DNA and that the putative helicase motif V/VI of the CSB may play a role in this process. The present study investigated the role of the CSB protein in cellular repair of 8-hydroxyadenine (8-OHAde), another abundant lesion in oxidatively damaged DNA. Extracts of CS-B-null cells and mutant cells with site-directed mutation in the motif VI of the putative helicase domain incised 8-hydroxyadenine in vitro less efficiently than wild type cells. Furthermore, CS-B-null and motif VI mutant cells accumulated more 8-hydroxyadenine in their genomic DNA than wild type cells after exposure to ␥-radiation at doses of 2 or 5 Gy. These results suggest that the CSB protein contributes to cellular repair of 8-OH-Ade and that the motif VI of the putative helicase domain of CSB is required for this activity.

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“…The best example is hydroxylation of 2'-deoxyguanosine at the C-8 position to produce 8-oxo-2'-deoxygaunosine. This modification not only completely suppresses the elimination of the deoxyribose moiety [22], which is used for recognizing deoxynucleoside ions, but it also changes the mechanism of pyrimidine ring decomposition. It can easily be envisioned that without prior knowledge, identification of this DNA oxidation product and its derivatives in a real sample might not be trivial.…”

Section: Introductionmentioning

confidence: 99%

Revisiting the Reactivity of Uracil During Collision Induced Dissociation: Tautomerism and Charge-Directed Processes

Beach

Gabryelski

2012

J. Am. Soc. Mass Spectrom.

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In our recent work towards the nontarget identification of products of nucleic acid (NA) damage in urine, we have found previous work describing the dissociation of NA bases not adequate to fully explain their observed reactivity. Here we revisit the gas-phase chemistry of protonated uracil (U) during collision induced dissociation (CID) using two modern tandem mass spectrometry techniques; quadrupole ion trap (QIT) and quadrupole time of flight (Q-TOF). We present detailed mechanistic proposals that account for all observed products of our experiments and from previous isotope labeling data, and that are supported by previous ion spectroscopy results and theoretical work. The diverse product-ions of U cannot be explained adequately by only considering the lowest energy form of protonated U as a precursor. The tautomers adopted by U during collisional excitation make it possible to relate the complex reactivity observed to reasonable mechanistic proposals and feasible product-ion structures for this small highly conjugated heterocycle. These reactions proceed from four different stable tautomers, which are excited to a specific activated precursor from which dissociation can occur via a charge-directed process through a favorable transition state to give a stabilized product. Understanding the chemistry of uracil at this level will facilitate the identification of new modified uracil derivatives in biological samples based solely on their reactivity during CID. Our integrated approach to describing ion dissociation is widely applicable to other NA bases and similar classes of biomolecules.

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Comparison of negative and positive ion electrospray tandem mass spectrometry for the liquid chromatography tandem mass spectrometry analysis of oxidized deoxynucleosides

Cited by 84 publications

References 25 publications

Differentiation of 2′-O- and 3′-O-methylated Ribonucleosides by tandem mass spectrometry

Differentiation of 2′-O- and 3′-O-methylated Ribonucleosides by tandem mass spectrometry

The Cockayne Syndrome Group B Gene Product Is Involved in Cellular Repair of 8-Hydroxyadenine in DNA

Revisiting the Reactivity of Uracil During Collision Induced Dissociation: Tautomerism and Charge-Directed Processes

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