Analysis of urinary modified nucleosides by mass spectrometry

Mass Spectrometry of Nucleosides and Nucleic Acids

Volumn , Issue , 2009, Pages 163-194

  Dudley, Ed ^a  

^a SWANSEA UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLATION; ALKYLATION; CARBON; MASS SPECTROMETRY; NUCLEOTIDES; RNA;

ANOMERIC CARBON; DNA STRUCTURE; METHYL GROUP; MODIFIED NUCLEOSIDES; NUCLEOBASES; PHOSPHATE GROUP; RNA MOLECULES; SUGAR MOIETY;

NUCLEIC ACIDS;

EID: 79955756432     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420044034     Document Type: Chapter

References (60)

1. Rozenski, J., Crain, P.F., and McCloskey, J.A. Nucleic Acids Res. 27, 196-197, 1999, http://library.med.utah.edu/RNAmods/
2. Dunin-Horkawicz, S., Czerwoniec, A., Gajda, M.J., Feder, M., Grosjean, H., and Bujnicki, J.M., MODOMICS: A database of RNA modification pathways, Nucleic Acids Res. 1(34), D145-9, 2006. http://modomics.genesilico.pl/
3. Edmonds, C.G. et al., Posttranslational modification of tRNA in thermophilic Archaea (Archaebacteria), J. Bacteriol. 173, 3138, 1991.
4. Rai, K. et al., Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development, Mol. Cell. Biol. 26, 7077, 2006.
5. Borek, E. et al., High turnover rate of transfer RNA in tumor tissue, Can. Res. 37, 3362, 1977.
6. Gehrke, C.W. et al., Patterns of urinary excretion of modified nucleosides, Can. Res. 39, 1150, 1979.
7. Borek, E., Modified nucleosides and cancer, Can. Res. 42, 2099, 1982.
8. Koshida, K. et al., Urinary modified nucleosides as tumor markers in cancer of the urinary organs or female genital tract, Urol. Res. 13, 213, 1985.
9. Nakano, K. et al., Urinary excretion of modified nucleosides as biological marker of RNA turnover in patients with cancer and AIDS, Clin. Chim. Acta 218, 169, 1993.
10. Tebib, J.G. et al., Relationship between urinary excretion of modified nucleosides and rheumatoid arthritis process, Br. J. Rheum. 36, 990, 1997.
11. Kawai, Y. et al., Endogenous formation of novel halogenated 2′-deoxycytidine. Hypohalous acidmediated DNA modification at the site of inflammation, J. Biol. Chem. 279, 51241, 2004.
12. Szabo, L.D. et al., Study of nucleic acid metabolism in two astronauts, Adv. Space Res. 4, 15, 1984.
13. Liebich, H.M. et al., Analysis of normal and modified nucleosides in urine by capillary electrophoresis, Chromatographia 24, 396, 1997.
14. Sasco, A.J. et al., Breast cancer prognostic significance of some modified urinary nucleosides, Can. Lett. 108, 157, 1996.
15. Hecht, S.M., Gupta, A.S., and Leonard, N.J., Mass spectra of nucleoside components of tRNA, Anal. Biochem. 30, 249, 1969.
16. McCloskey, J.A., Methods in Enzymology, Chapter 45, p. 193, Academic Press, New York, 1990.
17. Pang, H. et al., Mass spectrometry of nucleic acid constituents. Trimethylsilyl derivatives of nucleosides, J. Org. Chem. 47, 3924, 1982.
18. Crow, F.W. et al., Fast atom bombardment combined with tandem mass spectrometry for the determination of nucleosides, Anal. Biochem. 139, 243, 1984.
19. Dudley, E. et al., Analysis of urinary nucleosides I. Optimisation of high performance liquid chromatograghy/electrospray mass spectrometry, Rapid Commun. Mass Spectrom. 14, 1200, 2000.
20. Yen-Yang, Y., Charles, M.J., and Voyksner, R.D., Processes that affect electrospray ionization—mass spectrometry of nucleobases and nucleosides, J. Am. Soc. Mass Spectrom. 7, 1106, 1996.
21. Rice, J.M. and Dudek, G.O., Mass spectra of nucleic acid derivatives. II. Guanine, adenine and related compounds, J. Am. Chem. Soc. 89, 2719, 1967.
22. Nelson, C.C. and McCloskey, J.A., Collision-induced dissociation of uracil and its derivatives, J. Am. Soc. Mass Spectrom. 5, 339, 1994.
23. Gregson, J.M. and McCloskey, J.A., Collision-induced dissociation of protonated guanine, Int. J. Mass Spectrom. Ion Processes 165/166, 475, 1997.
24. Tuytten, R. et al., Intriguing mass spectrometric behaviour of guanosine under low energy collision induced dissociation: H2O adduct formation and gas phase reactions in the collision cell, J. Am. Soc. Mass Spectrom. 16, 1291, 2005.
25. Tuytten, R. et al., In-source CID of guanosine: Gas phase ion-molecule reactions, J. Am. Soc. Mass Spectrom. 17, 1050, 2006.
26. Jensen, S.S. et al., Collision induced dissociation of cytidine and its’ derivatives, J. Mass Spectrom. 6, 49, 2006.
27. Bagag, A., Giuliana, A., and Laprevote, O., Atmospheric pressure photoionization mass spectrometry of nucleic bases, ribonucleosides and ribonucleotides, Int. J. Mass Spectrom. 264, 1, 2007.
28. Bond, A.E. et al., Analysis of urinary nucleosides V. Identification of urinary pyrimidine nucleosides by liquid chromatography/electrospray mass spectrometry, Rapid Commun. Mass Spectrom. 20, 137, 2006.
29. Kammerer, B. et al., Mass spectrometric identification of modified urinary nucleosides used as potential biomedical markers by LC-ITMS coupling, Anal. Bioanal. Chem. 382, 1017, 2005.
30. Howlett, H.A. et al., Mass spectral analysis of modified ribonucleosides obtained by degradation of 14 alkali-stable dinucleotides isolated from yeast ribonucleic acid, Anal. Biochem. 39, 429, 1971.
31. Zhang, Q. and Wang, Y., Differentiation of 2′-O- and 3′-O-methylated ribonucleosides by tandem mass spectrometry, J. Am. Soc. Mass Spectrom. 17, 1096, 2006.
32. Rice, J.M. and Dudek, G.O., Mass spectra of uridine and pseudouridine: Fragmentation patterns characteristic of a carbon-carbon nucleosidic bond, Biochem. Biophys. Commun. 35, 383, 1969.
33. Felden, B. et al., Presence and location of modified nucleotides in Escherichia coli tmRNA: Structural mimicry with tRNA acceptor branches, EMBO J. 17, 3188, 1998.
34. Dudley, E. et al., 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, Rapid Commun. Mass Spectrom. 19, 3075, 2005.
35. Honda, I. et al., Creatinine at the evaluation of urinary 1-methyladenosine and pseudouridine excretion, Tohuku J. Exp. Med. 188, 133, 1999.
36. Narayanan, S. and Appleton, H.D., Creatinine: A review, Clin. Chem. 26, 1119, 1980.
37. Huskova, R. et al., Determination of creatinine in urine by tandem mass spectrometry, Clin. Chim. Acta 350, 99, 2004.
38. Taniai, H. et al., A simple quantitative assay for urinary adenosine using column switching high performance liquid chromatography, Tohuku J. Exp. Med. 208, 57, 2006.
39. Emmerechts, G., Herdewijn, P., and Rozenski, J., Pseudouridine detection improvement by derivatisation with methyl vinyl sulfone and capillary HPLC-mass spectrometry, J. Chromatogr. B 825, 233, 2005.
40. Böeseken, J., The use of boric acid for the determination of the configuration of carbohydrates, Adv. Carbohydr. Chem. Biochem. 4, 189, 1949.
41. Dudley, E. et al., Development of a purification procedure for the isolation of nucleosides from urine prior to mass spectrometric analysis, Nucleot. Nucleos. Nucleic Acids. 19, 545, 2000.
42. Sclimme, E. et al., Dual column HPLC analysis of modified ribonucleosides as urinary pathobiochemical markers in clinical research, Nucleos. Nucleot. 9, 407, 1993.
43. Tuytten, R. et al., The role of nitrogen Lewis basicity in boronate affinity chromatography of nucleosides, Anal. Chem., 79, 6662, 2007.
44. Esmans, E.L. et al., Direct liquid introduction LC/MS for the analysis of nucleoside material present in human urine, Biomed. Mass Spectrom. 12, 241, 1985.
45. Edmonds, C.G., Vestal, M.L., and McCloskey, J.A., Thermospray liquid chromatography-mass spectrometry of nucleosides and of enzymatic hydrolysates of nucleic acids, Nucleic Acids Res. 13, 8197, 1985.
46. Langridge, J.I. et al., Gas chromatography/mass spectrometric analysis of urinary nucleosides in cancer patients; Potential of modified nucleosides as tumour markers, Rapid Commun. Mass Spectrom. 7, 427, 1993.
47. Dudley, E. et al., Analysis of urinary nucleosides II. Comparison of mass spectrometric methods for the analysis of urinary nucleosides, Rapid Commun. Mass Spectrom. 15, 1701, 2001.
48. Takeda, N., Yoshizumi, H., and Toshimitsu, N., Detection and characterisation of modified nucleosides in serum and urine of uremic patients using capillary liquid chromatography-frit fast atom bombardment mass spectrometry, J. Chromatogr. B 746, 51, 2000.
49. Kammerer, B. et al., MALDI-TOF MS analysis of urinary nucleosides, J. Am. Soc. Mass Spectrom., 16, 940, 2005.
50. Liebich, H.M. et al., Chromatographic, capillary electrophoretic and matrix assisted laser desorption ionization time-of-flight mass spectrometry analysis of urinary modified nucleosides as tumor markers, J. Chromatogr. A 1071, 271, 2005.
51. Dudley, E. et al., Analysis of urinary nucleosides. III. Identification of 5′-deoxycytidine in urine of a patient with head and neck cancer, Rapid Commun. Mass Spectrom. 17, 1132, 2003.
52. Zhao, X. et al., Urinary profiling investigation of metabolites with cis-diol structure from cancer patients based on UPLC-MS and HPLC-MS as well as multivariate statistical analysis, J. Sep. Sci. 29, 2444, 2006.
53. Bullinger, D. et al., Identification of urinary nucleosides by ESI-TOF-MS, Bruker Appl. Book, 16, 2005.
54. Lee, S.H. et al., A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection, Rapid Commun. Mass Spectrom. 18, 973, 2004.
55. Dieterle, F. et al., Urinary nucleosides as potential tumor markers evaluated by learning vector quantization, Art. Intell. Med. 28, 265, 2003.
56. Seidel, P., Seidel, A., and Herbarth, O., Multilayer perceptron tumour diagnosis based on chromatography analysis of urinary nucleosides, Neur. Netw, 20, 646, 2007.
57. Sediel, A. et al., Modified nucleosides: An accurate tumour marker for clinical diagnosis of cancer, early detection and therapy control, Br. J. Cancer 94, 1726, 2006.
58. Chheda, G.B., Isolation and characterisation of N6-succinyladenosine from human urine, Nucleic Acids Res. 4, 739, 1977.
59. Dudley, E. et al., Analysis of urinary nucleosides IV. Identification of urinary purine nucleosides by liquid chromatography/electrospray mass spectrometry, Rapid Commun. Mass Spectrom. 18, 2730, 2004.
60. McCloskey, J.A., Methods in Enzymology, Chapter 41, p. 193, Academic Press, New York, 1990.