Stable isotope labeling for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay analysis of ribonucleic acids

Journal of Mass Spectrometry

Volumn 38, Issue 8, 2003, Pages 872-878

  Berhane, Beniam T ^a   Limbach, Patrick A ^a  

^a UNIVERSITY OF CINCINNATI   (United States)

Author keywords

Enzyme digestion; Matrix assisted laser desorption ionization mass spectrometry; Oligonucleotide sequencing; Post source decay; RNA

Indexed keywords

DESORPTION; IONIZATION; LASER APPLICATIONS; NUCLEIC ACIDS; OXYGEN;

LASER DESORPTION;

MASS SPECTROMETRY;

BUFFER; ENDONUCLEASE; HYDROGEN PEROXIDE; OLIGORIBONUCLEOTIDE; OXYGEN 18; RNA; WATER;

ARTICLE; CONTROLLED STUDY; ENZYMATIC DEGRADATION; FRAGMENTATION REACTION; ISOTOPE LABELING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; RADIOISOTOPE DECAY; RNA ANALYSIS; RNA CLEAVAGE; RNA PROCESSING;

ESCHERICHIA COLI; ISOTOPE LABELING; ISOTOPES; RIBONUCLEASES; RNA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 0042355182     PISSN: 10765174     EISSN: None     Source Type: Journal    
DOI: 10.1002/jms.504     Document Type: Article

References (49)

1. Limbach PA, Crain PF, McCloskey JA. Summary: the modified nucleosides in RNA. Nucleic Acids Res. 1994; 22: 2183.
2. Rozenski J, Crain PF, McCloskey JA. RNA modification database. Nucleic Acids Res. 1999; 27: 196.
3. Bjork GR, Ericson JU, Gustafsson CED, Hagervall TG, Jonsson YH, Wikstrom PM. tRNA Modifications. Annu. Rev. Biochem. 1987; 56: 263.
4. Stackebrandt E, Fowler VJ, Woese CR. A phylogenetic analysis of Lactobacilli, Pediococcus pentosaceus and Leuconostoc mesenteroides. Syst. Appl. Microbiol. 1983; 4: 326.
5. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 1977; 74: 5463.
6. Maxam AM, Gilbert W. A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA 1977; 74: 560.
7. Limbach PA. Indirect mass spectrometric methods for the characterization and sequencing of oligonucleotides. Mass Spectrom. Rev. 1996; 15: 297.
8. Nordhoff E, Kirpekar F, Roepstroff P. Mass spectrometry of nucleic acids. Mass Spectrom. Rev. 1997; 15: 69.
9. Kowalak JA, Pomerantz SC, Crain PF, McCloskey JA. A novel method for the determination of posttranscriptional modification in RNA by mass spectrometry. Nucleic Acids Res. 1993; 21: 4577.
10. Bakin A, Kowalak JA, McCloskey JA, Ofengand J. The single pseudouridine residue in Escherichia coli 16S RNA is located at position 516. Nucleic Acids Res. 1994; 22: 3681.
11. Kowalak JA, Dalluge JJ, McCloskey JA, Stetter KO. The role of posttranscriptional modification in stabilization of transfer-RNA from hyperthermophiles. Biochemistry 1994; 33: 7869.
12. Kowalak JA, Bruenger E, McCloskey JA. Posttranscriptional modification of the central loop of domain-V in Escherichia coli 23-S ribosomal-RNA. J. Biol. Chem. 1995; 270: 17 758.
13. Mangroo D, Limbach PA, McCloskey JA, Rajbhandary UL. An anticodon sequence mutant of Escherichia coli initiator transfer-RNA-possible importance of a newly acquired base modification next to the anticodon on its activity in initiation. J. Bacteriol. 1995; 177: 2858.
14. Sirumconnolly K, Peltier JM, Crain PF, McCloskey JA, Mason TL. Implications of a functional large ribosomal-RNA with only 3 modified nucleotides. Biochimie 1995; 77: 30.
15. Dalluge JJ, Hamamoto T, Horikoshi K, Morita RY, Stetter KO, McCloskey JA. Posttranscriptional modification of tRNA in psychrophilic bacteria. J. Bacteriol. 1997; 179: 1918.
16. Felden B, Hanawa K, Atkins JF, Himeno H, Muto A, Gesteland RF, McCloskey JA, Crain PF. Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches. EMBO J. 1998; 17: 3188.
17. Noon KR, Bruenger E, McCloskey JA. Posttranscriptional modifications in 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfataricus. J. Bacteriol. 1998; 180: 2883.
18. Kowalak J A, Bruenger E, Crain PF, McCloskey JA. Identities and phylogenetic comparisons of posttranscriptional modifications in 16 S ribosomal RNA from Haloferax volcanii. J. Biol. Chem. 2000; 275: 24484.
19. McCloskey JA, Graham DE, Zhou SL, Crain PF, Ibba M, Konisky J, Sell D, Olsen GJ. Post-transcriptional modification in archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales. Nucleic Acids Res. 2001; 29: 4699.
20. Kirpekar F, Douthwaite S, Roepstorff P. Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry. RNA 2000; 6: 296.
21. Hansen MA, Kirpekar F, Ritterbusch W, Vester B. Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria. RNA 2002; 8: 202.
22. Polo LM, Limbach PA. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the analysis of RNase H cleavage products. J. Mass Spectrom. 1998; 33: 1226.
23. Patteson KG, Rodicio LP, Limbach PA. Identification of the mass-silent posttranscriptionally modified nucleoside pseudouridine in RNA by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Nucleic Acids Res. 2001; 29: e49.
24. Berhane BT, Limbach PA. Functional microfabricated sample targets for marix-assisted laser desorption/ionization mass spectrometry analysis of ribonucleic acid. Anal. Chem. 2003; 75: 1997.
25. McLuckey SA, Van Berkel GJ, Glish GL. Tandem mass spectrometry of small, multiply charged oligonucleotides. J. Am. Soc. Mass Spectrom. 1992; 3: 60.
26. Ni J, Pomerantz SC, McCloskey JA. Rapid sequencing of modified oligonucleotides using tandem mass spectrometry with electrospray ionization. Nucleic Acids Symp. Ser. 1996; 35: 113.
27. McLafferty FW, Aaserud DJ, Guan Z, Little DP, Kelleher NL. Double stranded DNA sequencing by tandem mass spectrometry. Int. J. Mass Spectrom. Ion Processes 1997; 165/166: 457.
28. Talbo G, Mann M. Aspects of the sequencing of carbohydrates and oligonucleotides by matrix-assisted laser desorption/ionization post-source decay. Rapid Commun. Mass Spectrom. 1996; 10: 100.
29. Gross J, Leisner A, Hillenkamp F, Hahner S, Karas M, Schafer J, Lutzenkirchen F, Nordhoff E. Investigations of the metastable decay of DNA under ultraviolet matrix-assisted laser desorption/ionization conditions with post-Source-decay analysis and hydrogen/deuterium exchange. J. Am. Soc. Mass Spectrom. 1998; 9:866.
30. Gross J, Hillenkamp F, Wan KX, Gross ML. Metastable decay of negatively charged oligodeoxynucleotides analyzed with ultraviolet matrix-assisted laser desorption/ionization post-source decay and deuterium exchange. J. Am. Soc. Mass Spectrom. 2001; 12: 180.
31. Zhang L-K, Ren Y, Rempel D, Taylor JS, Gross ML. Determination of photomodified oligodeoxynucleotides by exonuclease digestion, matrix-assisted laser desorption/ionization and post-source decay mass spectrometry. J. Am. Soc. Mass Spectrom. 2001; 12: 1127.
32. Chou C-W, Limbach PA, Cole RB. Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange. J. Am. Soc. Mass Spectrom. 2002; 13: 1407.
33. Spengler B. Post-source decay analysis in matrix-assisted laser desorption/ionization mass spectrometry of biomolecules. J. Mass Spectrom. 1997; 32: 1019.
34. Desiderio DM, Kai M. Preparation of stable isotope-incorporated peptide internal standards for field desorption mass spectrometry quantification of peptides in biological tissue. Biomed. Mass Spectrom. 1983; 10: 471.
35. 2-interferon and identifies a proteolytically clipped γ-interferon that retains full antiviral activity. Biochem J. 1983; 215: 273.
36. Rose K, Simona MG, Savoy L-A, Offord RE, Wingfield P. C-Terminal identification by fast atom bombardment mass spectrometry. Biochem. J. 1988; 250: 253.
37. 18O water. Protein Sci. 2001; 10: 2251.
38. 18O-labeled water. Anal. Biochem. 1992; 205: 151.
39. Gaskell SJ, Haroldsen PE, Reilly MH. Collisionally activated decomposition of modified peptides using a tandem hybrid instrument. Biomed. Environ. Mass Spcctrom. 1988; 16: 31.
40. Takao T, Hori H, Okamoto K, Harada A, Kamachi M, Shimonishi Y. Facile assignment of sequence ions of a peptide labeled with O-18 at the carboxyl terminus. Rapid Commun. Mass Spectrom. 1991; 5: 312.
41. Schnolzer M, Jedrzejewski P, Lehmann WD. Protease-catalyzed incorporation of O-18 into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted desorption/ionization mass spectrometry. Electrophoresis 1996; 17: 945.
42. Shevchenko A, Chernushevich I, Ens W, Standing KC, Thomson B, Wilm M, Mann M. Rapid 'de novo' peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 1997; 11: 1015.
43. 18O-labeled internal standards. Rapid Commun. Mass Spectrom. 2000; 14: 1226.
44. 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal. Chem. 2001; 73: 2836.
45. 18O labeling: a tool for proteomics. Rapid Commun. Mass Spectrom. 2001; 15: 2456.
46. Shevchenko A, Shevchenko A. Evaluation of the efficiency of in-gel digestion of proteins by peptide isotopic labeling and MALDI mass spectrometry. Anal. Biochem. 2001; 296: 279.
47. 18O labeling for comparative proteomics: evaluation of endoprotease Glu-C as the catalytic agent. J. Proteome Res. 2002; 1: 27.
48. 18O labeling mass spectrometry for the rapid identification of marker/target proteins. Anal. Chem. 2001; 73: 3742.
49. Pomerantz SC, Kowalak JA, McCloskey JA. Determination of oligonucleotide composition from mass spectrometrically measured molecular weight. J. Am. Soc. Mass Spectrom. 1993; 4: 204.