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Ross RL, Yu N, Zhao R, Wood A, Limbach PA. Automated Identification of Modified Nucleosides during HRAM-LC-MS/MS using a Metabolomics ID Workflow with Neutral Loss Detection. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2785-2792. [PMID: 37948765 DOI: 10.1021/jasms.3c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The role of post-transcriptional modification in biological processes has been an ongoing field of study for several decades. Improvements in liquid chromatography platforms and mass spectrometry instrumentation have resulted in the enhanced identification, characterization, and quantification of modified nucleosides in biological systems. One consequence of the rapid technological improvements in the analytical acquisition of modified nucleosides has been a dearth of robust data processing workflows for analyzing more than a handful of samples at a time. To improve the utility of LC-MS/MS for batch analyses of modified nucleosides, a workflow for automated nucleoside identification has been developed. We adapted the Thermo Fisher Scientific metabolomics identification software package, Compound Discoverer, to accurately identify modified nucleosides from batch LC-MS/MS acquisitions. Three points of identification are used: accurate mass from a monoisotopic mass list, spectral matching from a spectral library, and neutral loss identification. This workflow was applied to a batch (n = 24) of urinary nucleosides, resulting in the accurate identification and relative quantification of 16 known nucleosides in less than 1 h.
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Affiliation(s)
- Robert L Ross
- Thermo Fisher Scientific, Lexington, Massachusetts 04241, United States
| | - Ningxi Yu
- Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Ruoxia Zhao
- Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Andrew Wood
- Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
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2
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Gosset-Erard C, Didierjean M, Pansanel J, Lechner A, Wolff P, Kuhn L, Aubriet F, Leize-Wagner E, Chaimbault P, François YN. Nucleos'ID: A New Search Engine Enabling the Untargeted Identification of RNA Post-transcriptional Modifications from Tandem Mass Spectrometry Analyses of Nucleosides. Anal Chem 2023; 95:1608-1617. [PMID: 36598775 DOI: 10.1021/acs.analchem.2c04722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As RNA post-transcriptional modifications are of growing interest, several methods were developed for their characterization. One of them established for their identification, at the nucleosidic level, is the hyphenation of separation methods, such as liquid chromatography or capillary electrophoresis, to tandem mass spectrometry. However, to our knowledge, no software is yet available for the untargeted identification of RNA post-transcriptional modifications from MS/MS data-dependent acquisitions. Thus, very long and tedious manual data interpretations are required. To meet the need of easier and faster data interpretation, a new user-friendly search engine, called Nucleos'ID, was developed for CE-MS/MS and LC-MS/MS users. Performances of this new software were evaluated on CE-MS/MS data from nucleoside analyses of already well-described Saccharomyces cerevisiae transfer RNA and Bos taurus total tRNA extract. All samples showed great true positive, true negative, and false discovery rates considering the database size containing all modified and unmodified nucleosides referenced in the literature. The true positive and true negative rates obtained were above 0.94, while the false discovery rates were between 0.09 and 0.17. To increase the level of sample complexity, untargeted identification of several RNA modifications from Pseudomonas aeruginosa 70S ribosome was achieved by the Nucleos'ID search following CE-MS/MS analysis.
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Affiliation(s)
- Clarisse Gosset-Erard
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg67000, France.,Université de Lorraine, LCP-A2MC, F-57000Metz, France
| | - Mévie Didierjean
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg67000, France
| | - Jérome Pansanel
- Université de Strasbourg, Institut Pluridisciplinaire Hubert Curien (IPHC), CNRS, UMR7178, Strasbourg67037, France
| | - Antony Lechner
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire, CNRS UPR9002, Université de Strasbourg, Strasbourg67084, France
| | - Philippe Wolff
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire, CNRS UPR9002, Université de Strasbourg, Strasbourg67084, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FR1589 CNRS, CEDEX, Strasbourg67084, France
| | | | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg67000, France
| | | | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg67000, France
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3
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Huang G, Ding Q, Xie D, Cai Z, Zhao Z. Technical challenges in defining RNA modifications. Semin Cell Dev Biol 2021; 127:155-165. [PMID: 34838434 DOI: 10.1016/j.semcdb.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/28/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023]
Abstract
It is well established that DNA base modifications play a key role in gene regulation during development and in response to environmental stress. This type of epigenetic control of development and environmental responses has been intensively studied over the past few decades. Similar to DNA, various RNA species also undergo modifications that play important roles in, for example, RNA splicing, protein translation, and the avoidance of immune surveillance by host. More than 160 different types of RNA modifications have been identified. In addition to base modifications, RNA modification also involves splicing of pre-mRNAs, leading to as many as tens of transcript isoforms from a single pre-RNA, especially in higher organisms. However, the function, prevalence and distribution of RNA modifications are poorly understood. The lack of a suitable method for the reliable identification of RNA modifications constitutes a significant challenge to studying their functions. This review focuses on the technologies that enable de novo identification of RNA base modifications and the alternatively spliced mRNA transcripts.
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Affiliation(s)
- Gefei Huang
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
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4
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Li Y, Zhou J, Yuan G. Discrimination of common isomerides of methyl nucleosides by collision-induced dissociation tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4594. [PMID: 32639684 DOI: 10.1002/jms.4594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/05/2020] [Accepted: 06/14/2020] [Indexed: 06/11/2023]
Abstract
The methyl-modified nucleosides (methyladenosine, methylguanosine, methylcytidine, and methyluridine) occur widely in nucleic acids and serve as biomarkers for a variety of types of diseases. Their isomers have the same parent ions in MS spectra and need further discrimination. Here, electrospray ionization mass spectrometry (ESI-MS) coupled with collision induced dissociation (CID) was used to distinguish the common isomerides of methyl-nucleosides. The various fragmentation patterns had been discussed in comparison of the different methyl modified nucleosides and were studied as a function of normalized collision energy. Then, structurally relevant fragments were obtained to efficiently identify characterization of methyl-nucleoside isomerides by collision induced dissociation. Therefore, this study provides a promising method using CID-MS for the discrimination of the isomeric methyl nucleosides, which could be useful to quantitative study of methyl nucleosides and detect of unknown methyl nucleosides.
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Affiliation(s)
- Yanru Li
- Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- School of Environment Science and Engineering, Tsinghua University, Beijing, 100084, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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Reim A, Ackermann R, Font-Mateu J, Kammel R, Beato M, Nolte S, Mann M, Russmann C, Wierer M. Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry. Nat Commun 2020; 11:3019. [PMID: 32541649 PMCID: PMC7295792 DOI: 10.1038/s41467-020-16837-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/27/2020] [Indexed: 11/09/2022] Open
Abstract
Transcription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the structure prediction of protein complexes but has been limited to the study of protein-protein and protein-RNA interactions. Here, we present a femtosecond laser-induced crosslinking mass spectrometry (fliX-MS) workflow, which allows the mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applied to recombinant histone octamers, NF1, and TBP in complex with DNA, our method is highly specific for the mapping of DNA binding domains. Identified crosslinks are in close agreement with previous biochemical data on DNA binding and mostly fit known complex structures. Applying fliX-MS to cells identifies several bona fide crosslinks on DNA binding domains, paving the way for future large scale ex vivo experiments.
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Affiliation(s)
- Alexander Reim
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Roland Ackermann
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Straße 15, 07745, Jena, Germany
| | - Jofre Font-Mateu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Robert Kammel
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Straße 15, 07745, Jena, Germany
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- University Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Stefan Nolte
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Straße 15, 07745, Jena, Germany
- Fraunhofer Institute for Applied Optics and Engineering (IOF), Albert-Einstein-Straße 7, 07745, Jena, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Christoph Russmann
- University of Applied Sciences and Arts Hildesheim/Holzminden/Goettingen (HAWK), Von-Ossietzky-Straße 99, 37085, Göttingen, Germany.
- Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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6
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Cui Y, Yuan J, Wang P, Wu J, Yu Y, Wang Y. Collision-Induced Dissociation Studies of Protonated Ions of Alkylated Thymidine and 2'-Deoxyguanosine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:927-937. [PMID: 32134268 PMCID: PMC7362892 DOI: 10.1021/jasms.9b00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mass spectrometry and tandem MS (MS/MS) have been widely employed for the identification and quantification of damaged nucleosides in DNA, including those induced by alkylating agents. Upon collisional activation, protonated ions of alkylated nucleosides frequently undergo facile neutral loss of a 2-deoxyribose in MS/MS, and further cleavage of the resulting protonated nucleobases in MS3 can sometimes be employed for differentiating regioisomeric alkylated DNA lesions. Herein, we investigated systematically the collision-induced dissociation (CID) of the protonated ions of O4-alkylthymidine (O4-alkyldT), O2-alkyldT, O6-alkyl-2'-deoxyguanosine (O6-alkyldG), and N2-alkyldG through MS3 analysis. The MS3 of O2- and O4-MedT exhibit different fragmentation patterns from each other and from other O2- and O4-alkyldT adducts carrying larger alkyl groups. Meanwhile, elimination of alkene via a six-membered ring transition state is the dominant fragmentation pathway for O2-alkyldT, O4-alkyldT, and O6-alkyldG adducts carrying larger alkyl groups, whereas O6-MedG mainly undergoes elimination of ammonia. The breakdown of N2-alkyldG is substantially influenced by the structure of the alkyl group, where the relative ease in eliminating ammonia and alkene is modulated by the chain length and branching of the alkyl groups. We also rationalize our observations with density functional theory (DFT) calculations.
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7
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Tang Y, Zhang JL. Recent developments in DNA adduct analysis using liquid chromatography coupled with mass spectrometry. J Sep Sci 2019; 43:31-55. [PMID: 31573133 DOI: 10.1002/jssc.201900737] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022]
Abstract
The formation of DNA adducts by genotoxic agents is an early event in cancer development, and it may lead to gene mutations, thereby initiating tumor development. The measurement of DNA adducts can provide critical information about the genotoxic potential of a chemical and its mechanism of carcinogenesis. In recent decades, liquid chromatography coupled with mass spectrometry has become the most important technique for analyzing DNA adducts. The improvements in resolution achievable with new chromatographic separation techniques coupled with the high specificity and sensitivity and wide dynamic range of new mass spectrometry systems have been used for both qualitative and quantitative analyses of DNA adducts. This review discusses the challenges in qualitative and quantitative analyses of DNA adducts by liquid chromatography coupled with mass spectrometry and highlights recent developments towards overcoming the limitations of liquid chromatography coupled with mass spectrometry methods. The key steps and new solutions, such as sample preparation, mass spectrometry fragmentation, and method validation, are summarized. In addition, the fundamental principles and latest advances in DNA adductomic approaches are reviewed.
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Affiliation(s)
- Yu Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
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8
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Electrooxidation of cytosine on bare screen-printed carbon electrodes studied by online electrochemistry-capillary electrophoresis-mass spectrometry. Electrochem commun 2019. [DOI: 10.1016/j.elecom.2018.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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9
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Jora M, Burns AP, Ross RL, Lobue PA, Zhao R, Palumbo CM, Beal PA, Addepalli B, Limbach PA. Differentiating Positional Isomers of Nucleoside Modifications by Higher-Energy Collisional Dissociation Mass Spectrometry (HCD MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1745-1756. [PMID: 29949056 PMCID: PMC6062210 DOI: 10.1007/s13361-018-1999-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 05/03/2023]
Abstract
The analytical identification of positional isomers (e.g., 3-, N4-, 5-methylcytidine) within the > 160 different post-transcriptional modifications found in RNA can be challenging. Conventional liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) approaches rely on chromatographic separation for accurate identification because the collision-induced dissociation (CID) mass spectra of these isomers nearly exclusively yield identical nucleobase ions (BH2+) from the same molecular ion (MH+). Here, we have explored higher-energy collisional dissociation (HCD) as an alternative fragmentation technique to generate more informative product ions that can be used to differentiate positional isomers. LC-MS/MS of modified nucleosides characterized using HCD led to the creation of structure- and HCD energy-specific fragmentation patterns that generated unique fingerprints, which can be used to identify individual positional isomers even when they cannot be separated chromatographically. While particularly useful for identifying positional isomers, the fingerprinting capabilities enabled by HCD also offer the potential to generate HPLC-independent spectral libraries for the rapid analysis of modified ribonucleosides. Graphical Abstract ᅟ.
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Affiliation(s)
- Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Andrew P Burns
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Peter A Lobue
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Cody M Palumbo
- Department of Chemistry, University of California, Davis, California, 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, California, 95616, USA
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA.
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10
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Chandran J, Aravind UK, Aravindakumar CT. Mass Spectrometric Characterization of Sonochemical Transformation Products of 2’-Deoxycytidine under Aerated Conditions: Direct Observation of Hydroxyhydroperoxide and Glycol. ChemistrySelect 2017. [DOI: 10.1002/slct.201700925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jisha Chandran
- Inter University Instrumentation Centre (IUIC); Mahatma Gandhi University; Kottayam, Kerala India
| | - Usha K. Aravind
- Advanced Centre of Environmental Studies and Sustainable Development (ACESSD); Mahatma Gandhi University; Kottayam, Kerala India
| | - Charuvila T. Aravindakumar
- Inter University Instrumentation Centre (IUIC); Mahatma Gandhi University; Kottayam, Kerala India
- Advanced Centre of Environmental Studies and Sustainable Development (ACESSD); Mahatma Gandhi University; Kottayam, Kerala India
- School of Environmental Sciences; Mahatma Gandhi University; Kottayam, Kerala India
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11
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Lu Z, Wang Q, Wang M, Fu S, Zhang Q, Zhang Z, Zhao H, Liu Y, Huang Z, Xie Z, Yu H, Gao X. Using UHPLC Q-Trap/MS as a complementary technique to in-depth mine UPLC Q-TOF/MS data for identifying modified nucleosides in urine. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1051:108-117. [PMID: 28340480 DOI: 10.1016/j.jchromb.2017.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 12/25/2022]
Abstract
Modified nucleosides, metabolites of RNA, are potential biomarkers of cancer before the appearance of morphological abnormalities. It is of great significance to comprehensively detect and identify nucleosides in human urine for discovery of cancer biomarkers. However, the lower abundance, the greater polarity and the matrix effects make it difficult to detect urinary nucleosides. In this paper, an integrated method consisted of sample preparation followed by ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC Q-TOF/MS) detection and primary identification, then ultra-high performance liquid chromatography coupled with hybrid triple quadrupole linear ion trap mass spectrometer (UHPLC Q-Trap/MS) further identification and validation were introduced. Firstly, to enrich the nucleosides and eliminate the urine matrix effects, different sorbent materials of solid phase extraction (SPE) and the elution conditions were screened. Secondly, UPLC Q-TOF/MS was used to acquire mass data in MSE mode. The structural formulas of nucleosides in urine sample were primarily identified according to retention time, accurate mass precursor ions and fragment ions from in-house database and online database. Thirdly, the preliminary identified nucleoside structures lacking of characteristic fragment ions were verified by UHPLC Q-Trap/MS in multiple reaction monitoring trigger enhanced product ion scan (MRM-EPI) and neutral loss scan (NL). At last, phenylboronic acid (PBA)-based SPE was utilized due to its higher MS signal and weaker matrix effects under optimized extraction conditions. Fifty-five nucleosides were primarily identified by UPLC Q-TOF/MS, among which 50 nucleosides were confirmed by UHPLC Q-Trap/MS. Five nucleosides, namely 4',5'-didehydro-5'-deoxyadenosine, 4',5'-didehydro-5'-deoxyinosine, isonicotinamide riboside, peroxywybutosine and hydroxywybutosine, were found from urine for the first time. The results will expand the Human Metabolome Database (HMDB).
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Affiliation(s)
- Zhiwei Lu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Qing Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Meiling Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Shuang Fu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Qingqing Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Zhixin Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Huizhen Zhao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Yuehong Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Zhenhai Huang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Ziye Xie
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Honghong Yu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Xiaoyan Gao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
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12
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Wang J, Liu M, Tong X, Peng W, Cao H, Su W. Chromatographic Fingerprint Analysis and Characterization of Constituents in Shenqi Fuzheng Injection by HPLC-DAD-ELSD and UFLC-DAD-Q-TOF Tandem Mass Spectrometry Techniques. ACTA CHROMATOGR 2015. [DOI: 10.1556/achrom.27.2015.3.11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Dudley E, Bond L. Mass spectrometry analysis of nucleosides and nucleotides. MASS SPECTROMETRY REVIEWS 2014; 33:302-31. [PMID: 24285362 DOI: 10.1002/mas.21388] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 05/12/2023]
Abstract
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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Affiliation(s)
- Ed Dudley
- Institute of Mass Spectrometry, College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
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14
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Sadr-Arani L, Mignon P, Chermette H, Douki T. Theoretical and experimental study of the fragmentation of protonated uracil. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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16
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Tishinov K, Schmidt K, Häussinger D, Gillingham DG. Structure-selective catalytic alkylation of DNA and RNA. Angew Chem Int Ed Engl 2012; 51:12000-4. [PMID: 23090851 DOI: 10.1002/anie.201205201] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Indexed: 01/17/2023]
Affiliation(s)
- Kiril Tishinov
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
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17
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Tishinov K, Schmidt K, Häussinger D, Gillingham DG. Structure-Selective Catalytic Alkylation of DNA and RNA. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205201] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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18
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Huybrechts T, Hermans M, Van Hoof B, Winderickx G, De Neef C, Hostyn S, Vrielynck S, Vermeulen W. Photochemical stability of 4'-azido-2'-deoxy-2'-methylcytidine hydrochloride: structural elucidation of major degradation products by LC-MS and NMR analysis. J Pharm Biomed Anal 2012; 70:231-44. [PMID: 22841557 DOI: 10.1016/j.jpba.2012.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/02/2012] [Accepted: 07/04/2012] [Indexed: 11/18/2022]
Abstract
The photochemical stability of (1'R,2'S,3'S,4'R)-4'-azido-2'-deoxy-2'-methylcytidine hydrochloride, a new anti-HCV agent, was investigated. Aqueous solutions and bulk drug powder of the drug candidate were exposed to UV-visible light, complying with ICH requirements. The nucleoside analog decomposed via loss of nitrogen to yield products derived from a highly reactive azide intermediate. Major photolysis products were identified by LC-MS and NMR analysis, revealing three main photodegradation pathways. The first one led to the formation of a ring-expanded imidate ester. The other degradation pathways involved exocyclic or endocyclic bond cleavage with imine or imino lactone formation. The latter were prone to rapid hydrolysis, eventually resulting in the release of cytosine, 2-methyl malonaldehyde and (E)-cytosyl-2-methylpropenal.
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Affiliation(s)
- Tom Huybrechts
- Pharmaceutical Development and Manufacturing Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium.
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Beach DG, Gabryelski W. Revisiting the reactivity of uracil during collision induced dissociation: tautomerism and charge-directed processes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:858-868. [PMID: 22351291 DOI: 10.1007/s13361-012-0343-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/13/2012] [Accepted: 01/17/2012] [Indexed: 05/31/2023]
Abstract
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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Affiliation(s)
- Daniel G Beach
- Department of Chemistry, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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20
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Giessing AMB, Kirpekar F. Mass spectrometry in the biology of RNA and its modifications. J Proteomics 2012; 75:3434-49. [PMID: 22348820 DOI: 10.1016/j.jprot.2012.01.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/20/2012] [Accepted: 01/26/2012] [Indexed: 01/31/2023]
Abstract
Many powerful analytical techniques for investigation of nucleic acids exist in the average modern molecular biology lab. The current review will focus on questions in RNA biology that have been answered by the use of mass spectrometry, which means that new biological information is the purpose and outcome of most of the studies we refer to. The review begins with a brief account of the subject "MS in the biology of RNA" and an overview of the prevalent RNA modifications identified to date. Fundamental considerations about mass spectrometric analysis of RNA are presented with the aim of detailing the analytical possibilities and challenges relating to the unique chemical nature of nucleic acids. The main biological topics covered are RNA modifications and the enzymes that perform the modifications. Modifications of RNA are essential in biology, and it is a field where mass spectrometry clearly adds knowledge of biological importance compared to traditional methods used in nucleic acid research. The biological applications are divided into analyses exclusively performed at the building block (mainly nucleoside) level and investigations involving mass spectrometry at the oligonucleotide level. We conclude the review discussing aspects of RNA identification and quantifications, which are upcoming fields for MS in RNA research. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
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Affiliation(s)
- Anders M B Giessing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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21
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Beach DG, Gabryelski W. Nontarget Analysis of Urine by Electrospray Ionization-High Field Asymmetric Waveform Ion Mobility-Tandem Mass Spectrometry. Anal Chem 2011; 83:9107-13. [DOI: 10.1021/ac202044h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel G. Beach
- Department of Chemistry, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Wojciech Gabryelski
- Department of Chemistry, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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22
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Krog JS, Español Y, Giessing AMB, Dziergowska A, Malkiewicz A, Ribas de Pouplana L, Kirpekar F. 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine is one of two novel post-transcriptional modifications in tRNALys(UUU) from Trypanosoma brucei. FEBS J 2011; 278:4782-96. [PMID: 22040320 DOI: 10.1111/j.1742-4658.2011.08379.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
tRNA is the most heavily modified of all RNA types, with typically 10-20% of the residues being post-transcriptionally altered. Unravelling the modification pattern of a tRNA is a challenging task; there are 92 currently known tRNA modifications, many of which are chemically similar. Furthermore, the tRNA has to be investigated with single-nucleotide resolution in order to ensure complete mapping of all modifications. In the present work, we characterized tRNA(Lys)(UUU) from Trypanosoma brucei, and provide a complete overview of its post-transcriptional modifications. The first step was MALDI-TOF MS of two independent digests of the tRNA, with RNase A and RNase T1, respectively. This revealed digestion products harbouring mass-changing modifications. Next, the modifications were mapped at the nucleotide level in the RNase products by tandem MS. Comparison with the sequence of the unmodified tRNA revealed the modified residues. The modifications were further characterized at the nucleoside level by chromatographic retention time and fragmentation pattern upon higher-order tandem MS. Phylogenetic comparison with modifications in tRNA(Lys) from other organisms was used through the entire analysis. We identified modifications on 12 nucleosides in tRNA(Lys)(UUU), where U47 exhibited a novel modification, 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine, based on identical chromatographic retention and MS fragmentation as the synthetic nucleoside. A37 was observed in two versions: a minor fraction with the previously described 2-methylthio-N(6)-threonylcarbamoyl-modification, and a major fraction with A37 being modified by a 294.0-Da moiety. The latter product is the largest adenosine modification reported so far, and we discuss its nature and origin.
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Affiliation(s)
- Jesper S Krog
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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23
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Juribašić M, Bellotto L, Traldi P, Tušek-Božić L. Electrospray ionization mass spectrometry of palladium(II) quinolinylaminophosphonate complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1815-1825. [PMID: 21952895 DOI: 10.1007/s13361-011-0186-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/27/2011] [Accepted: 05/27/2011] [Indexed: 05/31/2023]
Abstract
The mass spectrometric behavior of palladium(II) halide complexes of three types of quinolinylaminophosphonates, diethyl and dibutyl esters of [α-anilino-(quinolin-2-yl)methyl]phosphonic (L1, L2), [α-anilino-(quinolin-3-yl)methyl]phosphonic (L3, L4), and [α-(quinolin-3-ylamino)-N-benzyl]phosphonic acid (L5, L6), was investigated under positive ion electrospray ionization conditions. Each type of ligand forms complexes with different metal-ligand interactions. Mononuclear dihalide adducts cis-[Pd(L1/L2)X(2)] (1-4) and trans-[Pd(L3/L4)(2)X(2)] (5-8) as well as dinuclear tetrahalide complexes [Pd(2)(L5/L6)(3)X(4)] (9-12) (X=Cl, Br) are formed by metal bonding either through the quinoline or both the quinoline and amino nitrogen atoms. The sodiated molecule [M + Na](+) is observed in the mass spectra of all the complexes, and its abundance as well as the fragmentation pathway depend on the type of the complex. In the cis complexes (1-4) the initial decomposition goes under two fragmentation routes: those in which the sodium molecular adduct sequentially loses halides HX/NaX and those in which this loss is in the competition with the loss of dialkyl phosphite. The predominant pathways for decomposition of trans dihalide (5-8) and tetrahalide (9-12) complexes include three competitive reactions; the loss of halides, dialkyl phosphites and the intact phosphonate ligand molecule and its fragments formed by ester dissociation or complete loss of the phosphonate ester moiety. A series of acetonitrile adducts and cluster ions derived from dimolecular clusters [2M + Na](+) were also detected. The most important fragmentation patterns are rationalized and supported by the MS(n) studies.
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Affiliation(s)
- Marina Juribašić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia.
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Analysis of urinary nucleosides as potential tumor markers in human breast cancer by high performance liquid chromatography/electrospray ionization tandem mass spectrometry. Clin Chim Acta 2011; 412:1861-6. [DOI: 10.1016/j.cca.2011.06.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 06/19/2011] [Accepted: 06/21/2011] [Indexed: 02/08/2023]
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25
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Havelund JF, Giessing AMB, Hansen T, Rasmussen A, Scott LG, Kirpekar F. Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA. J Mol Biol 2011; 411:529-36. [PMID: 21723290 DOI: 10.1016/j.jmb.2011.06.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/17/2011] [Accepted: 06/20/2011] [Indexed: 10/18/2022]
Abstract
Complete characterization of a biomolecule's chemical structure is crucial in the full understanding of the relations between their structure and function. The dominating components in ribosomes are ribosomal RNAs (rRNAs), and the entire rRNA-but a single modified nucleoside at position 2501 in 23S rRNA-has previously been characterized in the bacterium Escherichia coli. Despite a first report nearly 20 years ago, the chemical nature of the modification at position 2501 has remained elusive, and attempts to isolate it have so far been unsuccessful. We unambiguously identify this last unknown modification as 5-hydroxycytidine-a novel modification in RNA. Identification of 5-hydroxycytidine was completed by liquid chromatography under nonoxidizing conditions using a graphitized carbon stationary phase in combination with ion trap tandem mass spectrometry and by comparing the fragmentation behavior of the natural nucleoside with that of a chemically synthesized ditto. Furthermore, we show that 5-hydroxycytidine is also present in the equivalent position of 23S rRNA from the bacterium Deinococcus radiodurans. Given the unstable nature of 5-hydroxycytidine, this modification might be found in other RNAs when applying the proper analytical conditions as described here.
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Affiliation(s)
- Jesper Foged Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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26
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Basic rules for the interpretation of atmospheric pressure ionization mass spectra of small molecules. J Chromatogr A 2010; 1217:3908-21. [DOI: 10.1016/j.chroma.2010.02.049] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 02/17/2010] [Accepted: 02/22/2010] [Indexed: 11/22/2022]
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27
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Kobetić R, Gembarovski D, Visnjevac A, Zinić B, Gabelica-Marković V. ESI-MS studies of palladium (II) complexes with 1-(p-toluenesulfonyl)cytosine/cytosinato ligands. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:51-64. [PMID: 19882593 DOI: 10.1002/jms.1688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The mononuclear complex Pd(1-TosC-N3)(2)Cl(2) (2) containing 1-(p-toluenesulfonyl)cytosine (1) as a ligand, as well as dinuclear complexes Pd(2)(1-TosC(-)-N3,N4)(4) (3) and Pd(2)(1-TosC(-)-N3,N4)(2)DMSO(2)Cl(2) (4) containing the ligand anion (1-TosC(-)), was mass analyzed by electrospray ionization ion trap MS/MS and high resolution MS. Complexes 3 and 4 were obtained by recrystallization of 2 from DMF and DMSO, respectively. The behavior of complex 2 in different solutions was monitored by electrospray ionization mass spectrometry (ESI-MS). Under the applied ESI-MS conditions, complex 2 in methanol reorganized itself dominantly as new complex 3 and the solvent did not coordinate the formed species. In H(2)O/DMSO, CH(3)CN/DMSO and CH(3)OH/DMSO solutions, complex 2 formed several new species with solvent molecules involved in their structure, e.g. complex 4 was formed as the major product. The newly formed species were also examined by LC-MS-DAD, confirming the solvent induced reorganization and the solution instability of complex 2.
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Affiliation(s)
- Renata Kobetić
- Division of Organic Chemistry and Biochemistry, Ruder Bosković Institute, Bijenicka cesta 54, 10 000 Zagreb, Croatia.
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28
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Cheng P, Li Y, Li S, Zhang M, Zhou Z. Collision-induced dissociation (CID) of guanine radical cation in the gas phase: an experimental and computational study. Phys Chem Chem Phys 2010; 12:4667-77. [DOI: 10.1039/b919513k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Reis A, Domingues MRM, Amado FML, Manuel Oliveira M, Domingues P. Detection and characterization of cyclic hydroxylamine adducts by mass spectrometry. Free Radic Res 2009; 42:481-91. [DOI: 10.1080/10715760802112783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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30
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Li HY, Wang SM, Liu HM, Bu SS, Li J, Han D, Zhang MZ, Wu GY. Separation and identification of purine nucleosides in the urine of patients with malignant cancer by reverse phase liquid chromatography/electrospray tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:641-51. [PMID: 19142897 DOI: 10.1002/jms.1539] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Urinary-modified nucleosides have a potential role as cancer biomarkers for a number of malignant diseases. High performance liquid chromatography (HPLC) was combined with full-scan mass spectrometry, MS/MS analysis and accurate mass measurements in order to identify purine nucleosides purified from urine. Potential purine nucleosides were assessed by their evident UV absorbance in the HPLC chromatogram and then further examined by the mass spectrometric techniques. In this manner, numerous modified purine nucleosides were identified in the urine samples from cancer patients including xanthine, adenosine, N1-methyladenosine, 5'-deoxy-5'-methylthioadenosine, 2-methyladenosine, N6-threonylcarbamoyladenosine, inosine, N1-methylinosine, guanosine, N1-methylguanosine, N7-methylguanine, N2-methylguanosine, N2,N2-dimethyguanosine, N2,N2,N7-trimethylguanosine. Furthermore, a number of novel purine nucleosides were tentatively identified via critical interpretation of the combined mass spectrometric data including N3-methyladenosine, N7-methyladenine, 5'-dehydro-2'-deoxyinosine, N3-methylguanine, O6-methylguanosine, N1,N2,N7-trimethylguanosine, N1-methyl-N2-ethylguanosine and N7-methyl-N1-ethylguanosine.
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Affiliation(s)
- Hua-Yu Li
- Department of Chemistry, Zhengzhou University, 100 Science Road, 450001 Zhengzhou, China
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31
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Cao H, Wang Y. Fragmentation of isomeric intrastrand crosslink lesions of DNA in an ion-trap mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:611-617. [PMID: 19103496 PMCID: PMC2691995 DOI: 10.1016/j.jasms.2008.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 11/24/2008] [Accepted: 11/25/2008] [Indexed: 05/27/2023]
Abstract
The collision-induced dissociation pathways of isomeric cytosine-guanine and cytosine-adenine intrastrand crosslink-containing dinucleoside monophosphates were investigated with the stable isotope-labeled compounds to gain insights into the effects of chemical structure on the fragmentation pathways of these DNA modifications. A Dimroth-like rearrangement, which was reported for protonated 2'-deoxycytidine and involved the switching of the exocyclic N4 with the ring N3 nitrogen atom, was also observed for the cytosine component in the protonated ions of C[5-8]G, C[5-2]A, and C[5-8]A, but not C[5-N(2)]G or C[5-N(6)]A. In these two sets of crosslinks, the C5 of cytosine is covalently bonded with its neighboring purine base via a carbon atom on the aromatic ring and an exocyclic nitrogen atom, respectively. On the contrary, the rearrangement could occur for the deprotonated ions of C[5-N(2)]G, C[5-N(6)]A, and unmodified cytosine, but not C[5-8]G, C[5-2]A, or C[5-8]A. In addition, ammonia could be lost more readily from C[5-N(2)]G and C[5-N(6)]A than from C[5-8]G, C[5-2]A, and C[5-8]A. The results from the present study afforded important guidance for the application of mass spectrometry for the structure elucidation of other intrastrand/interstrand crosslink lesions.
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Affiliation(s)
| | - Yinsheng Wang
- To whom correspondence should be addressed: Telephone: (951) 827-2700. Fax: (951) 827-4713. E-mail:
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Giessing AMB, Jensen SS, Rasmussen A, Hansen LH, Gondela A, Long K, Vester B, Kirpekar F. Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria. RNA (NEW YORK, N.Y.) 2009; 15:327-336. [PMID: 19144912 PMCID: PMC2648713 DOI: 10.1261/rna.1371409] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 10/28/2008] [Indexed: 05/27/2023]
Abstract
The Cfr methyltransferase confers combined resistance to five different classes of antibiotics that bind to the peptidyl transferase center of bacterial ribosomes. The Cfr-mediated modification has previously been shown to occur on nucleotide A2503 of 23S rRNA and has a mass corresponding to an additional methyl group, but its specific identity and position remained to be elucidated. A novel tandem mass spectrometry approach has been developed to further characterize the Cfr-catalyzed modification. Comparison of nucleoside fragmentation patterns of A2503 from Escherichia coli cfr+ and cfr- strains with those of a chemically synthesized nucleoside standard shows that Cfr catalyzes formation of 8-methyladenosine. In addition, analysis of RNA derived from E. coli strains lacking the m(2)A2503 methyltransferase reveals that Cfr also has the ability to catalyze methylation at position 2 to form 2,8-dimethyladenosine. The mutation of single conserved cysteine residues in the radical SAM motif CxxxCxxC of Cfr abolishes its activity, lending support to the notion that the Cfr modification reaction occurs via a radical-based mechanism. Antibiotic susceptibility data confirm that the antibiotic resistance conferred by Cfr is provided by methylation at the 8 position and is independent of methylation at the 2 position of A2503. This investigation is, to our knowledge, the first instance where the 8-methyladenosine modification has been described in natural RNA molecules.
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Reis A, Domingues MRM, Oliveira MM, Domingues P. Identification of free radicals by spin trapping with DEPMPO and MCPIO using tandem mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:689-703. [PMID: 19940335 DOI: 10.1255/ejms.1026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This study evaluates the use of a pyrroline (DEPMPO) and an imidazole (MCPIO) spin trap for the detection of hydroxyl and biomolecule (a peptide and a phospholipid) free radical adducts by Electrospray Ionization Mass Spectrometry (ESI-MS). The hydroxyl and biomolecule free radical adducts were detected using a QTOF and a linear ion trap (LIT) mass spectrometers. In the presence of hydroxyl radical, the mass spectrum obtained for each of the spin traps, DEPMPO and MCPIO, showed the presence of ions that could be attributed to hydroxyl and peroxyl radicals. Further characterisation by tandem mass spectrometry (ESI-MS/MS) revealed also the presence of hydroxy-hydroxyl adducts. Based on the results here described, we show that DEPMPO is a better spin trap for free radicals trapping and detection by mass spectrometry mainly because adducts show increased signal intensity. The ESI-MS spectra obtained for DEPMPO and MCPIO in the presence of biomolecule radicals (peptide and phospholipid) show molecular ions of DEPMPO and MCPIO adducts, which were characterised by tandem mass spectrometry. Both carbon centered radicals and oxygen centered radicals were efficiently trapped by the two spin traps and analysis of QTOF-MS/MS mass spectra allowed the location of the radical position in either the peptide or in the phospholipid fatty acyl chain. However, the tandem mass spectra of MCPIO adducts were more informative than DEPMPO adducts. The LIT-MS/MS spectra only shows typical peptide and phospholipid fragmentation, which difficult the structural characterisation of the spin adduct. In this study, the DEPMPO and MCPIO adducts were identified either in the nitrone or in the hydroxylamine form, which are ESR silent forms. The results described here show that both spin traps coupled with detection by mass spectrometry are valuable tools for trapping radicals of biomolecules. Furthermore, the acquired data provide valuable information on the presence of adducts (hydroxyl and biomolecule) that are Electron Spin Resonance (ESR) silent. This is especially important considering the complexity of the radical species in biological environment and the presence of reducing compounds that convert the spin adducts to silent ESR forms.
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Affiliation(s)
- Ana Reis
- Mass Spectrometry Center, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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34
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Development of a methodology utilizing gas chromatography ion-trap tandem mass spectrometry for the determination of low levels of caffeine in surface marine and freshwater samples. Anal Bioanal Chem 2008; 391:2635-46. [DOI: 10.1007/s00216-008-2174-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 04/28/2008] [Accepted: 05/05/2008] [Indexed: 10/22/2022]
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35
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:407-418. [PMID: 17326037 DOI: 10.1002/jms.1072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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