Abstract
Direct analysis in real time (DART) mass spectrometry is a recently developed innovative technology, which has shown broad applications for fast and convenient analysis of complex samples. Due to the ease of sample preparation, we have recently initiated an investigation of the feasibility of detecting nucleotides and nucleosides using the DART-AccuTOF instrument, which we will refer to as the DART mass spectrometer. Our experimental results reveal that the ions representing the intact molecules of nucleotides are not detectable in either positive-ion or negative-ion mode. Instead, all four natural nucleotides fragment in the DART ion source, and a common fragment ion, [C5H5O]+ (1), is observed, which is probably formed via multiple-elimination reactions. Interestingly, 1 can form adducts with nucleobases in different molar ratios in the DART ion source. In contrast to nucleotides, the ions representing the intact molecules of nucleosides are detected in both positive-ion and negative-ion mode using DART mass spectrometry. Surprisingly, the fragmentation pattern of nucleosides is different from that of nucleotides in the DART ion source. In the cases of nucleosides (under positive-ion conditions), the production of 1 is not observed, indicating that the phosphate group plays an important role for the multiple eliminations observed in the spectra of nucleotides. The in-source reactions described in the present work show the complexity of the conditions in the DART ion source, and we hope that our results illustrate a better understanding about DART mass spectrometry.
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Malins, D. C.; Hellstrom, K. E.; Anderson, K. M.; Johnson, P. M.; Vinson, M. A. Antioxidant-Induced Changes in Oxidized DNA. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5937–5941.
Kamiya, H. Mutagenic Potentials of Damaged Nucleic Acids Produced by Reactive Oxygen/Nitrogen Species: Approaches Using Synthetic Oligonucleotides and Nucleotides. Nucleic Acids Res. 2003, 31, 517–531.
Richter, C.; Park, J.-W.; Ames, B. N. Normal Oxidative Damage to Mitochondrial and Nuclear DNA Is Extensive. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 6465–6467.
Newton, R. P.; Kingston, E. E.; Overton, A. Mass Spectrometric Identification of Cyclic Nucleotides Released by the Bacterium Corynebacterium Murisepticum into the Culture Medium. Rapid Commun. Mass Spectrom. 1998, 12, 729–735.
Neeley, W. L.; Essigmann, J. M. Mechanisms of Formation, Genotoxicity, and Mutation of Guanine Oxidation Products. Chem. Res. Toxicol. 2006, 19, 491–505.
Collins, A. R.; Cadet, J.; Moeller, L.; Poulsen, H. E.; Vina, J. Are We Sure We Know How to Measure 8-Oxo-7,8-Dihydroguanine in DNA from Human Cells? Arch. Biochem. Biophys. 2004, 423, 57–65.
Cadet, J.; D’Ham, C.; Douki, T.; Pouget, J. P.; Ravanat, J. L.; Sauvaigo, S. Facts and Artifacts in the Measurement of Oxidative Base Damage to DNA. Free Radical Res. 1998, 29, 541–550.
Dizdaroglu, M.; Jaruga, P.; Rodriguez, H. Oxidative Damage to DNA: Mechanisms of Product Formation and Measurement by Mass Spectrometric Techniques. Crit. Rev. Oxidative Stress Aging 2003, 1, 165–189.
Holzl, G.; Herbert, O.; Pitsch, S.; Stutz, A.; Huber, C. G. Analysis of Biological and Synthetic Ribonucleic Acids by Liquid Chromatography-Mass Spectrometry Using Monolithic Capillary Columns. Anal. Chem. 2005, 77, 673–680.
Koc, H.; Swenberg, J. A. Applications of Mass Spectrometry for Quantitation of DNA Adducts. J. Chromatogr. B. 2002, 778, 323–343.
Cody, R. B.; Laramee, J. A.; Durst, H. D. Versatile New Ion Source for the Analysis of Materials in Open Air under Ambient Conditions. Anal. Chem. 2005, 77, 2297–2302.
Cody, R. B. Observation of Molecular Ions and Analysis of Nonpolar Compounds with the Direct Analysis in Real Time Ion Source. Anal. Chem. 2009, 81, 1101–1107.
McEwen, C. N.; Larsen, B. S. Ionization Mechanisms Related to Negative Ion APPI, APCI, and Dart. J. Am. Soc. Mass Spectrom. 2009, 20, 1518–1521.
Song, L.; Dykstra, A. B.; Yao, H.; Bartmess, J. E. Ionization Mechanism of Negative Ion-Direct Analysis in Real Time: A Comparative Study with Negative Ion-Atmospheric Pressure Photoionization. J. Am. Soc. Mass Spectrom. 2009, 20, 42–50.
Williams, J. P.; Patel, V. J.; Holland, R.; Scrivens, J. H. The Use of Recently Described Ionization Techniques for the Rapid Analysis of Some Common Drugs and Samples of Biological Origin. Rapid Commun. Mass Spectrom. 2006, 20, 1447–1456.
Vail, T. M.; Jones, P. R.; Sparkman, O. D. Rapid and Unambiguous Identification of Melamine in Contaminated Pet Food Based on Mass Spectrometry with Four Degrees of Confirmation. J. Anal. Toxicol. 2007, 31, 304–312.
Morlock, G.; Schwack, W. Determination of Isopropythioxanthone (ITX) in Milk, Yoghurt and Fat by HPTLC-FLD, HPTLC-ESI/MS, and HPTLC-DART/MS. Anal. Bioanal. Chem. 2006, 385, 586–595.
Haefliger, O. P.; Jeckelmann, N. Direct Mass Spectrometric Analysis of Flavors and Fragrances in Real Applications Using Dart. Rapid Commun. Mass Spectrom. 2007, 21, 1361–1366.
Borges, D. L. G.; Sturgeon, R. E.; Welz, B.; Curtius, A. J.; Mester, Z. Ambient Mass Spectrometric Detection of Organometallic Compounds Using Direct Analysis in Real Time. Anal. Chem. 2009, 81, 9834–9839.
Nilles, J. M.; Connell, T. R.; Durst, H. D. Quantitation of Chemical Warfare Agents Using the Direct Analysis in Real Time (Dart) Technique. Anal. Chem. 2009, 81, 6744–6749.
Kpegba, K.; Spadaro, T.; Cody, R. B.; Nesnas, N.; Olson, J. A. Analysis of Self-Assembled Monolayers on Gold Surfaces Using Direct Analysis in Real Time Mass Spectrometry. Anal. Chem. 2007, 79, 5479–5483.
Solano, E.; Stashenko, E.; Martinez, J.; Mora, U.; Kouznetsov, V. Ion [C5h5o]+ Formation in the Electron-Impact Mass Spectra of 4-Substituted-N-(2-Furylmethyl) Anilines. Relative Abundance Prediction Ability of the Dft Calulations. J. Mol. Struct. THEOCHEM 2006, 769, 83–85.
Moldoveanu, S. C. Analytical Pyrolysis of Natural Organic Polymers; Elsevier: New York, 1998; pp 399–407.
Laramee, J. A.; Cody, R. B.; Nilles, J. M.; Durst, H. D. Forensic Applications of DART (Direct Analysis in Real Time) Mass Spectrometry. In Forensic Analysis on the Cutting Edge; John Wiley and Sons, Inc.: Hoboken, NJ, 2007; pp 175–195.
Maleknia, S. D.; Vail, T. M.; Cody, R. B.; Sparkman, O. D.; Bell, T. L.; Adams, M. A. Temperature-Dependent Release of Volatile Organic Compounds of Eucalypts by Direct Analysis in Real Time (Dart) Mass Spectrometry. Rapid Commun. Mass Spectrom. 2009, 23, 2241–2246.
Wiebers, J. L.; Shapiro, J. A. Sequence Analysis of Oligodeoxyribonucleotides by Mass Spectrometry. 1. Dinucleotide Monophosphates. Biochemistry 1977, 16, 1044–1050.
Schulten, H.-R.; Beckey, H. D. Pyrolysis Field Desorption Mass Spectrometry of Deoxyribonucleic Acid. Anal. Chem. 1973, 45, 2358–2362.
Gross, M. L.; Lyon, P. A.; Dasgupta, A.; Gupta, N. K. Mass Spectral Studies of Probe Pyrolysis Products of Intact Oligoribonucleotides. Nucleic Acids Res. 1978, 5, 2695–2704.
Wiebers, J. L. Detection and Identification of Minor Nucleotides in Intact Deoxyribonucleic Acids by Mass Spectrometry. Nucleic Acids Res. 1976, 3, 2959–2970.
Abbas-Hawks, C.; Woorhees, K. J. In Situ Methylation of Nucleic Acids Using Pyrolysis/Mass Spectrometry. Rapid Commun. Mass Spectrom. 1996 10, 1802–1806.
Watson, J. T.; Sparkman, O. D. introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation: John Wiley and Sons, Inc.: Hoboken, NJ, 2007; p. 818.
McLuckey, S. A.; Habibi-Goudarzi, S. Decompositions of Multiply Charged Oligonucleotide Anions. J. Am. Chem. Soc. 1993, 115, 12085–12095.
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Curtis, M., Minier, M.A., Chitranshi, P. et al. Direct analysis in real time (DART) mass spectrometry of nucleotides and nucleosides: elucidation of a novel fragment [C5H5O]+ and its in-source adducts. J Am Soc Mass Spectrom 21, 1371–1381 (2010). https://doi.org/10.1016/j.jasms.2010.03.046
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DOI: https://doi.org/10.1016/j.jasms.2010.03.046