Collision-induced dissociation of uracil and its derivatives

Abstract

The collision-induced dissociation of protonated uracil has been studied by tandem mass spectrometry using models extensively labeled with stable isotopes, and derivatives of the kinds found in nucleic acids. Following collisional activation at 30 eV translational energy, protonated uracil dissociates through two principal pathways which do not occur in electron ionization mass spectra: (1) elimination of NH3 almost entirely from N-3, followed by loss of CO from C-4, 0(4); (2) loss of H2O, equally from 0(2) and 0(4). Elimination of HNCO, also the principal dissociation process from odd-electron molecular ions, proceeds primarily by loss of N-3, C-Z, O(2) and 10% from N-l, C-Z, 0(2). Several secondary dissociation products are formed with quantitative site specificity of skeletal atoms: C,HO+ (4-C0, C-5, C-6); H2CN+ (N-l, C-6); C2H2+ (N-l, C-5, C-6). First-step dissociation reactions are interpreted in terms of pyrimidine ring opening at likely sites of protonation after collisional activation of MH+. Collision-induced dissociation mass spectra of uracils with structural themes common to nucleic acids (methylation, replacement of 0 by S, C-5 substitution) follow analogous reaction paths which permit assignment of sites of substitution, and exhibit ion abundance changes attributed to differences in substituent basicity and electron density.

Revisiting the Reactivity of Uracil During Collision Induced Dissociation: Tautomerism and Charge-Directed Processes

“…Our first attempt to analyze a uracil standard by quadrupole time of flight (QTOF) and the quadrupole ion trap (QIT) showed a number of CID product-ions that had not been previously reported for uracil [16]. This was the result of an interfering isobaric m/z 113 ion contaminant present in the analyzed samples.…”

“…Accurate mass of product-ions allows us to confirm their elemental composition while sequential dissociation of product-ions provides information about their structure. By combining these results with previously published data from isotopic labeling [16], ion spectroscopy [26], and theoretical [26][27][28] studies, we present a more detailed description of the reactivity of U during CID than existed previously. This work will be of interest to those studying the CID of nucleic acids and those wishing to use tandem mass spectrometry for nontarget identification.…”

“…All collision energy (CE) values are presented in figure captions. In order to carry out the dissociation of protonated uracil at m/z 113, protonated uridine (m/z 245), which is known to produce abundant protonated uracil as its primary MS 2 dissociation product [12,16], was infused and selected in MS 2 . Protonated uracil at m/z 113 was then selected as the MS 3 precursor and its dissociation product selected as precursors in MS 4 .…”

“…All nucleosides and NA bases as well as a large number of their isotopically labeled analogues and modified species have been studied by CID [14][15][16][17][18]. These reports have allowed for the facile and selective detection of those target analytes in biological samples as well as some other compounds that showed similar fragmentation patterns.…”

“…In this paper, we revisit the gas-phase ion chemistry of protonated U. Uracil and several of its isotopologues has been previously analyzed by fast atom bombardment ionization with low energy CID [16]. However, the reactivity of this fundamental component of RNA is not yet fully understood.…”