[en] The fragmentation of the totally deuterated dinucleotide dAT(-) in labile positions (heteroatom-bound hydrogens) was compared for different MS/MS methods: CID, IRMPD, and EID. These experiments allowed us to affirm the coexistence of several fragmentation channels. They can be classified according to the involvement of nonlabile or labile protons in the fragmentation process. Moreover, double resonance experiments were performed in IRMPD and EID. They demonstrated the existence of consecutive fragmentation processes. The probability with which each channel is taken depends on the fragmentation technique used, i.e., the energy and the time scale of the method. The fragmentation channels that involve labile protons requiring peculiar three-dimensional structures are entropically unfavorable and enthalpically favorable. They are more observed in IRMPD and EID. The involvement of labile and, therefore, exchangeable protons in the fragmentation mechanism casts doubt on the use of tandem mass spectrometry to localize incorporated deuteriums in oligonucleotides.
Research Center/Unit :
Giga-Systems Biology and Chemical Biology - ULiège
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Bibliography
Jorgensen T.J.D., Gardsvoll H., Ploug M., and Roepstorff P. Intramolecular Migration of Amide Hydrogens in Protonated Peptides Upon Collisional Activation. J. Am. Chem. Soc. 127 (2005) 2785-2793
Rand K.D., and Jorgensen T.J.D. Development of a Peptide Probe for the Occurrence of Hydrogen (1H/2H) Scrambling Upon Gas-Phase Fragmentation. Anal. Chem. 79 (2007) 8686-8693
Rand K.D., Adams C.M., Zubarev R.A., and Jorgensen T.J.D. Electron Capture Dissociation Proceeds with a Low Degree of Intramolecular Migration of Peptide Amide Hydrogens. J. Am. Chem. Soc. 130 (2008) 1341-1349
Bache N., Rand K.D., Roepstorff P., and Jorgensen T.J.D. Gas-Phase Fragmentation of Peptides by MALDI In-Source Decay with Limited Amide Hydrogen (1H/2H) Scrambling. Anal. Chem. 80 (2008) 6431-6435
Zehl M., Rand K.D., Jensen O.N., and Jorgensen T.J.D. Electron Transfer Dissociation Facilitates the Measurement of Deuterium Incorporation into Selectively Labeled Peptides with Single Residue Resolution. J. Am. Chem. Soc. 130 (2008) 17453-17459
Wu J., and McLuckey S.A. Gas-Phase Fragmentation of Oligonucleotide Ions. Int. J. Mass Spectrom. 237 (2004) 197-241
Cerny R.L., Gross M.L., and Grotjahn L. Fast Atom Bombardment Combined with Tandem Mass Spectrometry for the Study of Dinucleotides. Anal. Biochem. 156 (1986) 424-435
Phillips D.R., and McCloskey J.A. A Comprehensive Study of the Low Energy Collision-Induced Dissociation of Dinucleoside Monophosphates. Int. J. Mass Spectrom. Ion Proceesses 128 (1993) 61-82
McLuckey S.A., and Habibi-Goudarzi S. Decompositions of Multiply-Charged Oligonucleotide Anions. J. Am. Chem. Soc. 115 (1993) 12085-12095
Rodgers M.T., Campbell S., Marzluff E.M., and Beauchamp J.L. Low-Energy Collision-Induced Dissociation of Deprotonated Dinucleotides-Determination of the Energetically Favored Dissociation Pathways and the Relative Acidities of the Nucleic-Acid Bases. Int. J. Mass Spectrom. Ion Processes 137 (1994) 121-149
Barry J.P., Vouros P., Vanschepdael A., and Law S.J. Mass and Sequence Verification of Modified Oligonucleotides Using Electrospray Tandem Mass-Spectrometry. J. Mass Spectrom. 30 (1995) 993-1006
Nordhoff E., Karas M., Cramer R., Hahner S., Hillenkamp F., Kirpekar F., Lezius A., Muth J., Meier C., and Engels J.W. Direct Mass-Spectrometric Sequencing of Low-Picomole Amounts of Oligodeoxynucleotides with up to 21 Bases by Matrix-Assisted Laser-Desorption Ionization Mass-Spectrometry. J. Mass Spectrom. 30 (1995) 99-112
Zhu L., Parr G.R., Fitzgerald M.C., Nelson C.M., and Smith L.M. Oligodeoxynucleotide Fragmentation in MALDI/TOF Mass-Spectrometry Using 355-Nm Radiation. J. Am. Chem. Soc. 117 (1995) 6048-6056
Wang Z., Wan K.X., Ramanathan R., Taylor J.S., and Gross M.L. Structure and Fragmentation Mechanisms of Isomeric T-Rich Oligodeoxynucleotides: A Comparison of Four Tandem Mass Spectrometric Methods. J. Am. Soc. Mass Spectrom. 9 (1998) 683-691
Gross J., Hillenkamp F., Wan K.X., and Gross M.L. 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. 12 (2001) 180-192
Wan K.X., Gross J., Hillenkamp F., and Gross M.L. Fragmentation Mechanisms of Oligodeoxynucleotides Studied by H/D Exchange and Electrospray Ionization Tandem Mass Spectrometry. J. Am. Soc. Mass Spectrom. 12 (2001) 193-205
Wan K.X., and Gross M.L. Fragmentation Mechanisms of Oligodeoxynucleotides: Effects of Replacing Phosphates with Methylphosphonates and Thymines with Other Bases in T-Rich Sequences. J. Am. Soc. Mass Spectrom. 12 (2001) 580-589
Liu J., Cao S., Jia B., Wei D., Liao X., Lu J., and Zhao Y. A Theoretical and Mass Spectrometry Study of the Novel Mechanism of N-Glycosidic Bond Cleavage in Nucleoside. Int. J. Mass Spectrom. 282 (2009) 1-5
Balbeur D., Dehareng D., and De Pauw E. Conformationally Driven Gas-Phase H/D Exchange of Dinucleotide Negative Ions. J. Am. Soc. Mass Spectrom. 18 (2007) 1827-1834
Sannes-Lowery K.A., and Hofstadler S.A. Sequence Confirmation of Modified Oligonucleotides Using IRMPD in the External Ion Reservoir of an Electrospray Ionization Fourier Transform Ion Cyclotron Mass Spectrometer. J. Am. Soc. Mass Spectrom. 14 (2003) 825-833
Keller K.M., and Brodbelt J.S. Collisionally Activated Dissociation and Infrared Multiphoton Dissociation of Oligonucleotides in a Quadrupole Ion Trap. Anal. Biochem. 326 (2004) 200-210
Kinet, C.; Gabelica, V.; Balbeur, D.; De Pauw, E. Electron Detachment Dissociation (EDD) Pathways in Oligonucleotides. Int. J. Mass Spectrom., in press.
Yang J., and Hakansson K. Characterization of Oligodeoxynucleotide Fragmentation Pathways in Infrared Multiphoton Dissociation and Electron Detachment Dissociation by Fourier Transform Ion Cyclotron Double Resonance. Eur. J. Mass Spectrom 15 (2009) 293-304
Wang B.H., and McLafferty F.W. Electron-Impact Excitation of Ions from Larger Organic-Molecules. Org. Mass Spectrom. 25 (1990) 554-556
Lioe H., and O'Hair R.A.J. Comparison of Collision-Induced Dissociation and Electron-Induced Dissociation of Singly Protonated Aromatic Amino Acids, Cystine and Related Simple Peptides Using a Hybrid Linear Ion Trap-FT-ICR Mass Spectrometer. Anal. Bioanal. Chem. 389 (2007) 1429-1437
Wolff J.J., Laremore T.N., Aslam H., Linhardt R.J., and Amster I.J. Electron-Induced Dissociation of Glycosaminoglycan Tetrasaccharides. J. Am. Soc. Mass Spectrom. 19 (2008) 1449-1458
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