Minimizing Base Loss and Internal Fragmentation in Collisionally Activated Dissociation of Multiply Deprotonated RNA

Journal of the American Society for Mass Spectrometry

Volumn 21, Issue 2, 2010, Pages 278-285

  Taucher, Monika ^a   Rieder, Ulrike ^a   Breuker, Kathrin ^a  

^a UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

BIO-MOLECULAR; CELLULAR FUNCTION; COLLISIONAL COOLING; COLLISIONALLY ACTIVATED DISSOCIATION; DE NOVO SEQUENCING; FRAGMENT IONS; GENE REGULATIONS; INTERNAL ENERGIES; ION PAIRS; MICRORNAS; NET CHARGES; PRECURSOR IONS; PRIMARY FRAGMENTS; RIBONUCLEIC ACID; RIBOSWITCHES; SMALL INTERFERING RNA; TOPDOWN;

DISSOCIATION; IONS; MASS SPECTROMETRY;

RNA;

RNA;

ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; FRAGMENTATION REACTION; GENETIC VARIABILITY; MOLECULAR SIZE; RNA CLEAVAGE; RNA SEQUENCE; RNA SYNTHESIS;

PROTONS; RNA, UNTRANSLATED; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; THERMODYNAMICS;

EID: 74249104622     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2009.10.010     Document Type: Article

References (22)

1. Limbach P.A., Crain P.F., and McCloskey J.A. Characterization of Oligonucleotides and Nucleic Acids by Mass Spectrometry. Curr. Opin. Biotechnol. 6 (1995) 96-102
2. Oberacher H., and Pitterl F. On the Use of ESI-QqTOF-MS/MS for the Comparative Sequencing of Nucleic Acids. Biopolymers 91 (2009) 401-409
3. Huang T., Liu J., Liang X., Hodges B.D.M., and McLuckey S.A. Collision-Induced Dissociation of Intact Duplex and Single-Stranded siRNA Anions. Anal. Chem. 80 (2008) 8501-8508
4. Bahr U., Aygün H., and Karas M. Sequencing of Single and Double Stranded RNA Oligonucleotides by Acid Hydrolysis and MALDI Mass Spectrometry. Anal. Chem. 81 (2009) 3173-3179
5. 18O Labeling. Int. J. Mass Spectrom. 234 (2004) 37-44
6. Farand J., and Gosselin F. De Novo Sequence Determination of Modified Oligonucleotides. Anal. Chem. 81 (2009) 3723-3730
7. Aebersold R., and Mann M. Mass Spectrometry-Based Proteomics. Nature 422 (2003) 198-207
8. Little D.P., Aaserud D.J., Valaskovic G.A., and McLafferty F.W. Sequence Information from 42-108-mer DNAs (Complete for a 50-mer) by Tandem Mass Spectrometry. J. Am. Chem. Soc. 118 (1996) 9352-9359
9. Han X., Jin M., Breuker K., and McLafferty F.W. Extending Top-Down Mass Spectrometry to Proteins with Masses Greater Than 200 Kilodaltons. Science 314 (2006) 109-112
10. Chait B.T. Mass Spectrometry: Bottom-Up or Top-Down?. Science 314 (2006) 65-66
11. McLuckey S.A., Van Berkel G.J., and Glish G.L. Tandem Mass Spectrometry of Small, Multiply Charged Oligonucleotides. J. Am. Soc. Mass Spectrom. 3 (1992) 60-70
12. Huang T., Kharlamova A., Liu J., and McLuckey S.A. Ion Trap Collision-Induced Dissociation of Multiply Deprotonated RNA: c/y-Ions versus (a-B)/w-Ions. J. Am. Soc. Mass Spectrom. 19 (2008) 1832-1840
13. Tromp J.M., and Schürch S. Gas-Phase Dissociation of Oligoribonucleotides and Their Analogs Studied by Electrospray Ionization Tandem Mass Spectrometry. J. Am. Soc. Mass Spectrom. 16 (2005) 1262-1268
14. Schürch S., Bernal-Mendez E., and Leumann C.J. Electrospray Tandem Mass Spectrometry of Mixed-Sequence RNA/DNA Oligonucleotides. J. Am. Soc. Mass Spectrom. 13 (2002) 936-945
15. Tromp J.M., and Schürch S. Electrospray Ionization Tandem Mass Spectrometry of Biphenyl-Modified Oligo(Deoxy)ribonucleotides. Rapid Commun. Mass Spectrom. 20 (2006) 2348-2354
16. Micura R. Small Interfering RNAs and Their Chemical Synthesis. Angew. Chem. Int. Ed. 41 (2002) 2265-2269
17. 1 Riboswitch Aptamers. Chem. BioChem. 10 (2009) 1141-1144
18. Gabelica V., and de Pauw E. Internal Energy and Fragmentation of Ions Produced in Electrospray Sources. Mass Spectrom. Rev. 24 (2005) 566-587
19. 1, Lacks a Phosphate as Deprotonation Site and cannot be Detected.
20. Hoaglund C.S., Liu Y., Ellington A.D., Pagel M., and Clemmer D.E. Gas-Phase DNA: Oligothymidine Ion Conformers. J. Am. Chem. Soc. 119 (1997) 9051-9052
21. Moradian A., Scalf M., Westphall M.S., Smith L.M., and Douglas D.J. Collision Cross Sections of Gas Phase DNA Ions. Int. J. Mass Spectrom. 219 (2002) 161-170
22. Cheng X., Gale D.C., Udseth H.R., and Smith R.D. Charge State Reduction of Oligonucleotide Negative Ions from Electrospray Ionization. Anal. Chem. 67 (1995) 586-593