A comprehensive study of the low energy collision-induced dissociation of dinucleoside monophosphates

Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange

“…In H/D exchange experiments, the matrix molecules, solvents, and oligonucleotide molecules have gone through virtually complete H/D exchange prior to MALDI analysis. In agreement with the literature (e.g., ESI/MS/MS [50], MALDI-PSD [28]), the source of the hydrogens is the nonexchangeable hydrogen on the sugar moiety. During decomposition, the w 3 ϩ ion preferentially obtained two hydrogens and the [a 3 -B 3 ] ϩ ion obtained a single hydrogen.…”

Cleavage reactions of the complex ions derived from self-complementary deoxydinucleotides and alkali-metal ions using positive ion electrospray ionization with tandem mass spectrometry

“…Various mass spectrometric methods have been used to characterize metal ion biomolecular interaction at the molecular level, to determine the site of metal ion attachment to the biomolecular and its effect on altering the properties and reactivities of the biomolecule [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17]. ESI-MS was shown to be an excellent means for characterizing of oligonucleotides [18,19], and provide unambiguous identification of singly and multiplycharged ions of deprotonated, protonated, and metalated oligonucleotides.…”

“…The dissociation reactions of protonated molecular ions from 12 possible hetero-deoxyribonucleotides were previously studied using fast atom bombardment with tandem mass spectrometry [5,6]. It was proposed…”

“…The dissociation reactions of protonated molecular ions from 12 possible hetero-deoxyribonucleotides were previously studied using fast atom bombardment with tandem mass spectrometry [5,6]. It was proposed that dissociation reactions of positive ions are influenced by a tertiary structure in which the phosphate oxygens, stabilized by interactions with the 3Ј-terminus base.…”

Arrhenius activation parameters for the loss of neutral nucleobases from deprotonated oligonucleotide anions in the gas phase

“…Elucidating these mechanisms is of practical importance, since it will facilitate the rational development of MS-based techniques for sequencing. In addition, the dissociation of biomolecules in the gas phase reflects their intrinsic properties, which are of fundamental interest.For oligodeoxynucleotides (ODNs), sequence information can be obtained from the fragmentation behaviour of either the protonated or deprotonated gaseous ions and the dissociation behaviour of both forms has been extensively investigated [1][2][3][4][5][6][7][8][9][10]. The dissociation of deprotonated ODNs, the focus of the present study, has been shown to proceed first by the loss of a nucleobase, adenine (A), guanine (G), cytosine (C) or thymine (T), in its neutral or deprotonated form, followed by fragmentation of the phosphoester bond at the deoxyribose 3Ј C™O bond at the site of base loss to produce (a-base) and w type ions, according to the nomenclature proposed by McLuckey and coworkers [7].…”