Atmospheric pressure MALDI-FTMS of normal and chemically modified RNA

Journal of the American Society for Mass Spectrometry

Volumn 16, Issue 2, 2005, Pages 199-207

  Kellersberger, Katherine A ^a   Yu, Eizadora T ^a   Merenbloom, Samuel I ^a   Fabris, Daniele ^a  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DECOMPOSITION; DNA; FOURIER TRANSFORMS; MASS SPECTROMETRY; PROTEINS; RNA; SOLVENTS;

FEMTOMOLE QUANTITIES; FOURIER TRANSFORM MASS SPECTROMETRY (FTMS); HYDROLYTIC FRAGMENTS; ISOTOPIC DISTRIBUTION;

ATMOSPHERIC PRESSURE;

DNA; NUCLEASE; NUCLEIC ACID; POLY(DIALLYLDIMETHYLAMMONIUM CHLORIDE); RNA;

ALGORITHM; ARTICLE; ATMOSPHERIC PRESSURE MATRIX ASSISTED LASER DESORPTION IONIZATION FOURIER TRANSFORM MASS SPECTROMETRY; DNA DETERMINATION; FOURIER TRANSFORM MASS SPECTROMETRY; MASS SPECTROMETRY;

ATMOSPHERIC PRESSURE; BASE SEQUENCE; FOURIER ANALYSIS; MAMMARY TUMOR VIRUS, MOUSE; RIBONUCLEASES; RNA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 13444293122     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2004.10.008     Document Type: Article

References (69)

1. K. Tanaka, H. Ido, Y. Yoshida, T. Yoshida Detection of high mass molecules by laser desorption time-of-flight mass spectrometry 1987 Proceedings of the Second Japan-China Joint Symposium on Mass Spectrometry; Osaka, Japan, September 15-18
2. M. Karas, F. Hillenkamp Laser desorption ionization of proteins with molecular masses exceeding 10,000 Daltons Anal. Chem. 60 1988 2299 2301
3. R. Hettich, M. Buchanan Structural characterization of normal and modified oligonucleotides by matrix-assisted laser desorption Fourier transform mass spectrometry J. Am. Soc. Mass Spectrom. 2 1991 402 412
4. E. Nordhoff, R. Cramer, M. Karas, F. Hillenkamp, F. Kirpekar, K. Kristiansen, P. Roepstorff Ion stability of nucleic acids in infrared matrix-assisted laser desorption/ionization mass spectrometry Nucleic Acids Res. 21 1993 3347 3357
5. E. Nordhoff, F. Kirpekar, P. Roepstorff Mass spectrometry of nucleic acids Mass Spectrom. Rev. 15 1996 67 138
6. K. Schneider, B.T. Chait Matrix-assisted laser desorption mass spectrometry of homopolymer oligodeoxyribonucleotides. Influence of base composition on the mass spectrometric response Org. Mass Spectrom. 28 1993 1353
7. F. Kirpekar, E. Nordhoff, K. Kristiansen, P. Roepstorff, A. Lezius, S. Hahner, M. Karas, F. Hillenkamp Matrix assisted laser desorption/ionization mass spectrometry of enzymatically synthesized RNA up to 150 kDa Nucleic Acids Res. 22 1994 3866-3370
8. K.J. Wu, T.A. Shaler, C.H. Becker Time-of-flight mass spectrometry of underivatized single-stranded DNA oligomers by matrix-assisted laser desorption Anal. Chem. 66 1994 1637 1645
9. E.A. Stemmler, M.V. Buchanan, G.B. Hurst, R.L. Hettich Analysis of modified oligonucleotides by matrix-assisted laser desorption/ionization Fourier transform mass spectrometry Anal. Chem. 67 1995 2924 2930
10. P. Juhasz, M.T. Roskey, I.P. Smirnov, L.A. Haff, M.L. Vestal, S.A. Martin Applications of delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry to oligonucleotide analysis Anal. Chem. 68 1996 941 946
11. G. Talbo, M. Mann Aspects of the sequencing of carbohydrates and oligonucleotides by matrix-assisted laser desorption/ionization post-source decay Rapid Commun. Mass Spectrom. 10 1996 100 103
12. J. Gross, A. Leisner, F. Hillenkamp, S. Hahner, M. Karas, J. Schäfer, F. Lützenkirchen, E. Nordhoff 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. 9 1998 866 878
13. W. Tang, L. Zhu, L.M. Smith Controlling DNA fragmentation in MALDI-MS by chemical modification Anal. Chem. 69 1997 302 312
14. E. Nordhoff, M. Karas, R. Cramer, S. Hahner, F. Hillenkamp, F. Kirpekar, A. Lezius, J. Muth, C. Meier, J.W. Engels J. Mass Spectrom. 30 1995 99 112
15. L. Zhu, G.R. Parr, M.C. Fitzgerald, C.M. Nelson, L.M. Smith Oligodeoxynucleotide fragmentation in MALDI/TOF mass spectrometry using 355-nm radiation J. Am. Chem. Soc. 117 1995 6048 6056
16. C.L. Hendrickson, M.R. Emmett, A.G. Marshall Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry Annu. Rev. Phys. Chem. 50 1999 517 536
17. M.B. Comisarow, A.G. Marshall Fourier transform ion cyclotron resonance Chem. Phys. Lett. 1974 282 283
18. R.J. Cotter Time-of-flight mass spectrometry for the structural analysis of biological molecules Anal. Chem. 64 1992 1027A
19. R.J. Cotter Time-of-flight mass spectrometry. Instrumentation and applications in biological research 1997 ACS Professional Reference Books Washington, DC
20. M.V. Buchanan, R.L. Hettich Fourier transform mass spectrometry of high-mass biomolecules Anal. Chem. 65 1993 245A 259A
21. E.A. Stemmler, R.L. Hettich, G.B. Hurst, M.V. Buchanan Matrix-assisted laser desorption/ionization Fourier-transform mass spectrometry of oligodeoxyribonucleotides Rapid Commun. Mass Spectrom. 7 1993 828 836
22. Y. Li, K. Tang, D.P. Little, H. Koster, R.L. Hunter, R.T.J. McIver High-resolution MALDI Fourier transform mass spectrometry of oligonucleotides Anal. Chem. 68 1996 2090 2096
23. J.A. Castoro, C. Köster, C.L. Wilkins Matrix-assisted laser desorption/ionization of high-mass molecules by Fourier-transform mass spectrometry Rapid Commun. Mass Spectrom. 6 1992 239
24. C. Köster, J.A. Castoro, C.L. Wilkins High-resolution matrix-assisted laser desorption/ionization by Fourier transform mass spectrometry J. Am. Chem. Soc. 114 1992 7572 7574
25. D.L. Rempel, M.L. Gross High pressure trapping in Fourier transform mass spectrometry A radiofrequency-only-mode event J. Am. Soc. Mass Spectrom. 3 1992 590
26. L. Schweikhard, S. Guan, A.G. Marshall Quadrupolar excitation and collisional cooling for axialization and high pressure trapping of ions in Fourier transform ion cyclotron resonance mass spectrometry Int. J. Mass Spectrom. Ion Proc. 120 1992 71 83
27. T. Solouki, D.H. Russell Laser desorption studies of high mass biomolecules in Fourier-transform ion cyclotron resonance mass spectrometry Proc. Natl. Acad. Sci. U.S.A. 89 1992 5701 5704
28. S. Guan, M.C. Whal, T.D. Wood, A.G. Marshall Enhanced mass resolving power, sensitivity, and selectivity in laser desorption Fourier transform ion cyclotron resonance mass spectrometry by ion axialization and cooling Anal. Chem. 65 1993 1753
29. L. Pasa-Tolic, S. Huang, S. Guan, H.S. Kim, A.G. Marshall Ultrahigh-resolution matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectra of peptides J. Mass Spectrom. 30 1995 825
30. S.J. Pastor, J.A. Castoro, C.L. Wilkins High-mass analysis using quadrupolar excitation/ion cooling in a Fourier transform mass spectrometer Anal. Chem. 67 1995 379 384
31. J. Yao, M. Dey, S.J. Pastor, C.L. Wilkins Analysis of high-mass biomolecules using electrostatic fields and matrix-assisted laser desorption/ionization in a Fourier transform mass spectrometer Anal. Chem. 67 1995 3638 3642
32. R.T.J. McIver, Y. Li, R.L. Hunter High-resolution laser desorption mass spectrometry of peptides and small proteins Proc. Natl. Acad. Sci. U.S.A. 91 1994 4801 4805
33. J. Wu, S.T. Fannin, M.A. Franklin, T.F. Molinski, C.B. Lebrilla Exact mass determination for elemental analysis of ions produced by matrix-assisted laser desorption Anal. Chem. 67 1995 3788 3792
34. R.M. Heeren, J.J. Boon Rapid microscale analyses with an external ion source Fourier transform ion cyclotron resonance mass spectrometer Int. J. Mass Spectrom. Ion Proc. 157/158 1996 391 403
35. G. Baykut, R. Jertz, M. Witt Matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry with pulsed in-source collision gas and in-source ion accumulation Rapid Commun. Mass Spectrom. 14 2000 1238 1247
36. P.B. O'Connor, C.E. Costello A high pressure matrix-assisted laser desorption/ionization Fourier transform mass spectrometry ion source for thermal stabilization of labile biomolecules Rapid Commun. Mass Spectrom. 15 2001 1862 1868
37. P.B. O'Connor, B.A. Budnik, V.B. Ivleva, P. Kaur, S.C. Moyer, J.L. Pittman, C.A. Costello A high pressure matrix-assisted laser desorption ion source for Fourier transform mass spectrometry designed to accommodate large targets with diverse surfaces J. Am. Soc. Mass Spectrom. 15 2004 128 132
38. A.N. Krutchinsky, A.V. Loboda, V.L. Spicer, R. Dworschak, W. Ens, K.G. Standing Orthogonal injection of matrix-assisted laser desorption/ionization ions into a time-of -flight spectrometer through a collisional damping interface Rapid Commun. Mass Spectrom. 12 1998 508 518
39. V.V. Laiko, A.L. Burlingame U.S. Patent 5965884 1999
40. V.V. Laiko, M.A. Baldwin, A.L. Burlingame Atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry Anal. Chem. 72 2000 652 657
41. M. Yamashita, J.B. Fenn Electrospray ion source. Another variation on the free-jet theme J. Phys. Chem. 88 1984 4671 4675
42. D.J. Harvey, R.H. Bateman, R. Bordoli, R. Tyldesley Ionization and fragmentation of complex glycans with a quadrupole time-of-flight mass spectrometer fitted with a matrix-assisted laser desorption/ionization source Rapid Commun. Mass Spectrom. 14 2000 2135 2142
43. J.A. McLean, W.K. Russell, D.H. Russell A high repetition rate (1 kHz) microcrystal laser for high throughput atmospheric pressure MALDI-quadrupole time-of-flight mass spectrometry Anal. Chem. 75 2003 648 654
44. V.V. Laiko, S.C. Moyer, R.J. Cotter Atmospheric pressure MALDI/ion trap mass spectrometry Anal. Chem. 72 2000 5239 5243
45. V.V. Laiko, N.I. Taranenko, V.D. Berkout, B.D. Musselman, V.M. Doroshenko Atmospheric pressure laser desorption/ionization on porous silicon Rapid Commun. Mass Spectrom. 16 2002 1737 1742
46. S.C. Moyer, R.J. Cotter, A.S. Woods Fragmentation of phosphopeptides by atmospheric pressure MALDI and ESI/ion trap mass spectrometry J. Am. Soc. Mass Spectrom. 13 2001 274 283
47. M.C. Galicia, A. Vertes, J.H. Callahan Atmospheric pressure matrix-assisted laser desorption/ionization in transmission geometry Anal. Chem. 74 2002 1891 1895
48. C.A. Miller, D. Yi, P.D. Perkins An atmostpheric pressure matrix-assisted laser desorption/ionization ion trap with enhanced sensitivity Rapid commun. Mass spectrom. 17 2003 860 868
49. J.-L. Wolfender, F. Chua, H. Ball, F. Wolfender, M. Fainzilber, M.A. Baldwin, A.L. Burlingame Identification of tyrosine sulfation in Conus pennaceus conotoxins α-PnIA and α- PIB Further investigation of labile sulfo- and phosphopeptides by electrospray, matrix-assisted laser desorption/ ionization (MALDI) mass spectrometry J. Mass Spectrom. 34 1999 447 454
50. T. Keough, M.P. Lacey, R.J. Strife Atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry of sulfonic acid derivatized tryptic peptides Rapid Commun. Mass Spectrom. 15 2001 2227 2239
51. C.S. Creaser, J.C. Reynolds, D.J. Harvey Structural analysis of oligosaccharides by atmospheric pressure matrix-assisted laser desorption/ionization quadrupole ion trap mass spectrometry Rapid Commun. Mass Spectrom. 16 2002 176 184
52. A.J. Madonna, K.J. Voorhees Detection of cyclic lipopeptide biomarkers from Bacillus species using atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry Anal. Chem. 75 2003 1628 1637
53. K.A. Kellersberger, P.V. Tan, V.V. Laiko, V.M. Doroshenko, D. Fabris Atmospheric pressure MALDI-Fourier transform mass spectrometry Anal. Chem. 66 2004 3930 3934
54. E. Yu, D. Fabris Direct probing of RNA structures and RNA-protein interactions in the HIV-1 packaging signal by chemical modification and electrospray ionization Fourier transform mass spectrometry J. Mol. Biol. 330 2003 211 223
55. V.M. Doroshenko, V.V. Laiko, N.I. Taranenko, V.D. Berkhout, H.S. Lee Recent developments in atmospheric pressure MALDI mass spectrometry Int. J. Mass Spectrom. Ion Proc. 221 2002 39 58
56. S.C. Moyer, L.A. Marzilli, A.S. Woods, V.V. Laiko, V.M. Doroshenko, R.J. Cotter Atmospheric pressure matrix-assisted laser desorption/ionization (AP MALDI) on a quadrupole ion trap mass spectrometer Int. J. Mass Spectrom. Ion Proc. 226 2003 133 150
57. P.V. Tan, V.V. Laiko, V.M. Doroshenko Atmospheric pressure MALDI with pulsed dynamic focusing for high-efficiency transmission of ions into a mass spectrometer Anal. Chem. 75 2004 2462 2469
58. K. Sannes-Lowery, R.H. Griffey, G.H. Kruppa, J.P. Speir, S.A. Hofstadler Multipole storage assisted dissociation, a novel in-source dissociation technique for electrospray ionization generated ions Rapid Commun. Mass Spectrom. 12 1998 1957 1961
59. L.J. de Koning, N.M.M. Nibbering, S.L. van Orden, F.H. Laukien Mass selection of ions in a Fourier transform ion cyclotron resonance trap using correlated harmonic excitation fields (CHEF) Int. J. Mass Spectrom. Ion Proc. 165/166 1997 209 219
60. J.W. Gauthier, T.R. Trautman, D.B. Jacobson Sustained off-resonance irradiation for collision-activated dissociation involving Fourier transform mass spectrometry. Collision-activated dissociation technique that emulates infrared multiphoton dissociation Anal. Chim. Acta 246 1991 211 225
61. Y. Kim, G.B. Hurst, M.J. Doktycz, M.V. Buchanan Improving spot homogeneity by using polymer substrates in matrix-assisted laser desorption/ionization mass spectrometry of oligonucleotides Anal. Chem. 73 2001 2617 2624
62. I.P. Smirnov, L.R. Hall, P.L. Ross, L.A. Haff Applications of DNA-binding polymers for preparation of DNA for analysis by matrix-assisted laser desorption/ionization mass spectrometry Rapid Commun. Mass Spectrom. 15 2001 1427 1432
63. Y. Xu, M.L. Bruening, J.T. Watson Use of polymer-modified MALDI-MS probes to improve analyses of protein digests and DNA Anal. Chem. 76 2004 3106 3111
64. U. Pieles, W. Zurcher, M. Schar, H.E. Moser Matrix-assisted laser desorption ionization time-of-flight mass spectrometry a powerful tool for the mass and sequence analysis of natural and modified oligonucleotides Nucleic Acids Res. 21 1993 3191 3196
65. D.P. Little, T.J. Cornish, M.J. O'Donnell, A. Braun, R.J. Cotter, H. Köster MALDI on a chip; Analysis of arrays of low-femtomole to subfemtomole quantities of synthetic oligonucleotides and DNA diagnostic products dispensed by a piezoelectric pipet Anal. Chem. 69 1997 4540 4546
66. Y. Xu, J.T. Watson, M.L. Bruening Patterned monolayer/polymer films for analysis of dilute or salt-contaminated protein samples by MALDI-MS Anal. Chem. 75 2003 185 190
67. R.T. Batey, R.P. Rambo, J.A. Doudna Tertiary motifs in RNA structure and folding Angew. Chem. Int. Ed. Engl. 38 1999 2326 2343
68. K.A. Kellersberger, E. Yu, G.H. Kruppa, M.M. Young, D. Fabris Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation Anal. Chem. 76 2004 2438 2445
69. T.E. Yu, Q. Zhang, D. Fabris Untying the FIV frameshifting pseudoknot structure by MS3D J. Mol. Biol. 345 2005 69 80