Increased sequence coverage of thymine-rich oligodeoxynucleotides by infrared multiphoton dissociation compared to collision-induced dissociation

Journal of Mass Spectrometry

Volumn 45, Issue 10, 2010, Pages 1098-1103

  Parr, Carol ^a   Brodbelt, Jennifer S ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Collision induced dissociation; DNA; Infrared multiphoton dissociation; Oligonucleotide; Thymine

Indexed keywords

CLEAVAGE SITES; COLLISION-INDUCED DISSOCIATION; INFRARED MULTIPHOTON DISSOCIATION; ION TRAP MASS SPECTROMETER; MASS SPECTRA; NUCLEOBASES; OLIGODEOXYNUCLEOTIDES; SECONDARY DISSOCIATION; THYMINE; THYMINE BASE;

DIAGNOSTIC PRODUCTS; MASS SPECTROMETERS; MASS SPECTROMETRY; OLIGONUCLEOTIDES;

DISSOCIATION;

NUCLEIC ACID BASE; OLIGODEOXYNUCLEOTIDE; THYMINE;

ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; DISSOCIATION; FRAGMENTATION REACTION; INFRARED SPECTROMETRY; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

INFRARED RAYS; MASS SPECTROMETRY; OLIGODEOXYRIBONUCLEOTIDES; PHOTONS; SEQUENCE ANALYSIS, DNA; THYMINE;

EID: 78650837653     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.1780     Document Type: Article

References (16)

1. D. P. Little, D. J. Aaserud, G. A. Valaskovic, F. W. McLafferty. Sequence information from 42-108-mer DNAs (complete for a 50-mer) by tandem mass spectrometry. J. Am. Chem. Soc. 1996, 118(39), 9352.
2. J. Ni, S. C. Pomerantz, J. Rozenski, Y. Zhang, J. A. McCloskey. Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry. Anal. Chem. 1996, 68(13), 1989.
3. Z. Wang, K. X. Wan, R. Ramanathan, J. S. Taylor, M. L. Gross. Structure and fragmentation mechanisms of isomeric T-rich oligodeoxynucleotides: A comparison of four tandem mass spectrometric methods. J. Am. Soc. Mass Spectrom. 1998, 9(7), 683.
4. S. Pan, K. Verhoeven, J. K. Lee. Investigation of the initial fragmentation of oligodeoxynucleotides in a quadrupole ion trap: Charge level-related base loss. J. Am. Soc. Mass Spectrom. 2005, 16(11), 1853.
5. K. X.Wan, M. L. Gross. Fragmentation mechanisms of oligodeoxynucleotides: Effects of replacing phosphates with methylphosphonates and thymines with other bases in T-rich sequences. J. Am. Soc.Mass Spectrom. 2001, 12(5), 580.
6. A. Favre, F. Gonnet, J. Tabet. Location of the negative charge(s) on the backbone of single-stranded deoxyribonucleic acid in the gas phase. Eur. J.Mass Spectrom. 2000, 6(5), 389.
7. S. A. McLuckey, S. Habibi-Goudarzi. Decompositions of multiply charged oligonucleotide anions. J. Am. Chem. Soc. 1993, 115(25), 12085.
8. J. Yang, K. Hakansson. Characterization of oligodeoxynucleotide fragmentation pathways in infrared multiphoton dissociation and electron detachment dissociation by Fourier transform ion cyclotron double resonance. Eur. J.Mass Spectrom. 2009, 15(2), 293.
9. K. M. Keller, J. S. Brodbelt. Collisionally activated dissociation and infrared multiphoton dissociation of oligonucleotides in a quadrupole ion trap. Anal. Biochem. 2004, 326(2), 200.
10. K. Hakansson, R. R. Hudgins, A. G. Marshall, R. A. J. O'Hair. Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications. J. Am. Soc. Mass Spectrom. 2003, 14(1), 23.
11. J. Yang, J. Mo, J. T. Adamson, K. Hakansson. Characterization of oligodeoxynucleotides by electron detachment dissociation Fourier transform ion cyclotron resonancemass spectrometry. Anal. Chem. 2005, 77(6), 1876.
12. S. I. Smith, J. S. Brodbelt. Electron transfer dissociation of oligonucleotide cations. Int. J. Mass Spectrom. 2009, 283(1-3), 85.
13. R. Daneshfar, J. S. Klassen. Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the Arrhenius parameters for neutral base loss. J.Am. Soc. Mass Spectrom. 2006, 17(9), 1229.
14. R. Daneshfar, J. S. Klassen. Arrhenius activation parameters for the loss of neutral nucleobases from deprotonated oligonucleotide anions in the gas phase. J. Am. Soc.Mass Spectrom. 2004, 15(1), 55.
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. 1995, 117(22), 6048.
16. M. W. Gardner, L. A. Vasicek, S. Shabbir, E. V. Anslyn, J. S. Brodbelt. Chromogenic cross-linker for the characterization of protein structure by infrared multiphoton dissociation mass spectrometry. Anal. Chem. 2008, 80(13), 4807.