Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

Abstract

We report electron capture dissociation (ECD) and infrared multiphoton dissociation (IRMPD) of doubly protonated and protonated/alkali metal ionized oligodeoxynucleotides. Mass spectra following ECD of the homodeoxynucleotides polydC, polydG, and polydA contain w or d "sequence" ions. For polydC and polydA, the observed fragments are even-electron ions, whereas radical w/d ions are observed for polydG. Base loss is seen for polydG and polydA but is a minor fragmentation pathway in ECD of polydC. We also observe fragment ions corresponding to w/d plus water in the spectra of polydC and d(GCATGC). Although the structure of these ions is not clear, they are suggested to proceed through a pentavalent phosphorane intermediate. The major fragment in ECD of d(GCATGC) is a d ion. Radical a-or z-type fragment ions are observed in most cases. IRMPD primarily results in base loss, but backbone fragmentation is also observed. IRMPD provides more sequence information than ECD, but the spectra are more complex due to extensive base and water losses. It is proposed that the smaller degree of sequence coverage in ECD, with fragmentation mostly occurring close to the ends of the molecules, is a consequence of a mechanism in which the electron is captured at a P¢O bond, resulting in a negatively charged phosphate group. Consequently, at least two protons (or alkali metal cations) must be present to observe a w or d fragment ion, a requirement that is less likely for small fragments. , in which a parent ion is first isolated from other ions of different mass-to-charge (m/z) ratio and then dissociated into sequence-specific fragment ions. The fragmentation technique (e.g., collision induced dissociation (CID) [6], infrared multiphoton dissociation (IRMPD) [7,8], blackbody infrared radiative dissociation (BIRD) [9,10], surface induced dissociation (SID) [11], or ultraviolet photodissociation [12,13]) as well as the nature of the parent ion charge (singly versus multiply charged, protonation versus metal cation attachment, cation versus anion, etc.) play key roles in determining the major fragmentation processes.To date most attention has focused on the fragmentation reactions of even-electron ions, but electrospray ionization in combination with ion-ion reactions, ionelectron reactions, or ion-neutral reactions have opened up new opportunities to examine the fragmentation reactions of odd-electron ions. Examples include electron capture dissociation (ECD) of [M ϩ nH] nϩ ions of peptides and proteins [14,15], polymers [16,17] [24], and CID of a Cu(II)-amine-peptide complex [25]. In each case, the formation of the radical cation (or anion) results in new fragmentation pathways, which are complementary to those observed for even-electron fragmentation. For example, disulfide bond cleavage is observed as a major fragmentation pathway in ECD [26], whereas such cleavage is not observed in CID or IRMPD. In other instances, novel fragmentation chem-

Characterization of phosphate-containing metabolites by calcium adduction and electron capture dissociation

“…Interestingly, these product ions are also observed in SORI-CAD of both the ATP and the GTP complex, demonstrating that neutral base loss is a very low energy fragmentation pathway, comparable to dissociation of the noncovalent interactions in these complexes. The fact that guanine loss can occur without loss of either water molecule suggests that this pathway requires less activation energy than adenine loss, consistent with the nucleic acid MS/MS literature, which contains ample evidence of guanine as the most labile nucleobase in both ECD [45,60,61] and CAD [62].…”

“…Unique product ions were also observed in SORI-CAD, including Ca 2ϩ -adducted phosphate species (related to mass 97 and 177, Figure 5a= and b=) providing information about the number of phosphate groups. Thus, as previously demonstrated for a range of biomolecules [45][46][47][48], ECD and SORI-CAD provide complementary structural information about metabolite cations.…”

“…For example, labile post translational modifications in peptides and proteins can be localized with ECD, whereas they are preferentially lost in CAD, thereby precluding their localization [38, 40 -43]. ECD has also been shown to yield complementary structural information compared to CAD for other macromolecules, including oligonucleotides [45,46], lantibiotics [47], and a siderophore [48].…”

Tandem time-of-flight mass spectrometer for photodissociation of biopolymer ions generated by matrix-assisted laser desorption ionization (MALDI-TOF-PD-TOF) using a linear-plus-quadratic potential reflectron

“…Infrared multiphoton dissociation (IRMPD) [13,14] has been used to induce dissociation of biopolymer ions also, even though a large amount of internal energy needed for such a dissociation necessitates absorption of a large number of infrared photons. When electronic transitions of chromophores by ultraviolet radiation are utilized, the number of photons that must be absorbed can be far smaller than in IRMPD.…”

Top-down identification and characterization of biomolecules by mass spectrometry

“…Their net charge in solution is negative, resulting in significantly lower ion yields using ESI of the opposite polarity [63]. However, ECD of doubly-protonated nucleic acids [64] or CAD of multiply-charged protein anions [7] can provide useful structural information. An alternative to ECD is electron detachment dissociation (EDD) [61], which has been applied to negatively charged ions of polypeptides [65] and nucleic acids [66,67].…”