Fragmentation reactions of all 64 protonated trimer oligodeoxynucleotides and 16 mixed base tetramer oligodeoxynucleotides via tandem mass spectrometry in an ion trap

Vrkic, Ana K.; O’Hair, Richard A. J.; Foote, Simon J.; Reid, Gavin E.

doi:10.1016/s1387-3806(99)00150-5

Cited by 41 publications

(46 citation statements)

References 29 publications

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“…As expected, no molecular ions were observed in the positive ion mode for dT 6 , due to its low proton affinity [52,80]. Consequently, it was not possible to examine its ECD or IRMPD fragmentation patterns.…”

Section: Fragmentation Of Polydeoxythymidinementioning

confidence: 82%

“…The [M ϩ H] ϩ ion is most likely a result of hydrogen atom (H⅐) ejection from [M ϩ 2H] ϩ⅐ . In all polydC spectra, two of the major fragment ions can be identified as consecutive backbone "sequence" ions, of either the w-or d-type [38,52]. It is not possible to distinguish between those two ion types based on mass alone because of the symmetry of polydC (i.e., the nucleotide sequence is identical when read from the 5' or 3' end).…”

Section: Ecd Of Doubly Protonated Polydeoxycytidinementioning

confidence: 99%

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Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

Håkansson

Hudgins

Marshall

et al. 2003

J. Am. Soc. Mass Spectrom.

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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-

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Section: Fragmentation Of Polydeoxythymidinementioning

confidence: 82%

Section: Ecd Of Doubly Protonated Polydeoxycytidinementioning

confidence: 99%

Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

Håkansson

Hudgins

Marshall

et al. 2003

J. Am. Soc. Mass Spectrom.

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“…If the internal energy of those fragment ions remains high, the remaining energy will randomize within the fragment ion and will have finite possibility of undergoing a base loss reaction. In the CID of oligonucleotides [8b, 35,41], base loss from those protonated fragment ions can occur via two different possible pathways (E 1 and E 2 mechanisms). Similarly, w n ϩ and d n ϩ fragments might also undergo E 1 or E 2 reactions to form the [wn -C]ϩ and [dn -C]ϩ fragment ions.…”

Section: Oligonucleotides Positive Identificationmentioning

confidence: 99%

A mechanistic study of the electron capture dissociation of oligonucleotides

Chan

Choy

Chan

et al. 2009

J. Am. Soc. Mass Spectrom.

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Electron capture dissociation (ECD) of a series of custom-synthesized oligonucleotide pentamers was performed in a Fourier-transform mass spectrometer with a conventional filamenttype electron gun. Dissociation of oligonucleotide ions by electron capture generates primarily w/d-type and z/a-type ions with and without the loss of a nucleobase fragment ions. Minor yields of radical [z/a ϩ H]· fragment ions were also observed in many cases. It is interesting to note that some nucleoside-like fragment ions and protonated nucleobase ions (except thymine-related nucleobases and nucleoside-like fragments) were observed in most ECD spectra. The formation of these low-mass fragment ions was tentatively attributed to the secondary fragmentation of the radical S tructural characterization of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) is important, as DNA and RNA play important roles in many biochemical processes. Even with the completion of the human genome project, the importance of studying nucleic acid remains. For instance, a large region of DNA requires re-sequencing [1] to allow the detection and characterization of nucleotide mutation. There is a constant demand for powerful and rapid analytical methods to determine the structure of nucleic acids and their constituents. With the development of "soft" desorption/ionization techniques, matrix-assisted laser desorption/ionization (MALDI) [2,3] and electrospray ionization (ESI) [4,5] methods, mass spectrometry has become an indispensable, quick, and reliable tool for the analysis of oligonucleotides [6]. However, simple mass measurement provides little structural information for confirmation of the sequence for unknown natural and synthetic oligonucleotides. Much research effort has recently been devoted to the development of various tandem mass spectrometry (MS/MS) methods for structural elucidation of biomolecules. The critical event in tandem mass spectrometry of biomolecules is the activation of the selected precursor ions to induce unimolecular dissociation. Common ion activation methods used for analysis of biomolecules include lowand high-energy collision-induced dissociation (CID) [7, 8], surface-induced dissociation (SID) [9], infrared multiphoton dissociation (IRMPD) [10], and blackbody infrared radiative dissociation (BIRD) [11]. However, fragment ions observed in the tandem mass spectra using these ion activation methods mostly originate from cleavages of weak bonds [12].A relatively new ion activation method, electron capture dissociation (ECD) [13] has demonstrated several interesting features. For example, for protein-type biomolecules, ECD leads predominantly to the dissociation of the N-C ␣ linkage even in the presence of labile post-translational modifications [14,15]. A combination of ECD and other dissociation methods, such as IRMPD and CID, has been shown to provide complementary information for unambiguous identification of the type and the position of several important protein posttranslational modifications [16 -18] and for de novo s...

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“…Ni et al, 1996;Vrkic et al, 2000;Kirpekar & Krogh, 2001;Wan et al, 2001), and the resulting production spectra are well predictable on the basis of known fragmentation pathways. The nomenclature for oligonucleotide fragment ions proposed by McLuckey, Berkel, & Glish (1992) is now generally utilized to identify ions and ion series of sequence-relevance.…”

Section: B Lc-tandem Ms For Sequence Determinationmentioning

confidence: 99%

Analysis of nucleic acids by on‐line liquid chromatography–Mass spectrometry

Huber

Oberacher

2001

Mass Spectrometry Reviews

143

129

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The numerous problems posed by modern biochemistry, biology, and medicine, as well as the growing significance of genetic engineering require the application of fast and reliable methods of utmost sensitivity and selectivity for the analysis of nucleic acids. High-performance liquid chromatography (HPLC) and mass spectrometry (MS) represent established analytical techniques for the characterization and structural elucidation of single- and double-stranded nucleic acids, ranging in size from a few nucleotides to several thousand base pairs. Although both techniques are independently applicable for nucleic acid analysis, the on-line hyphenation significantly enhances their potential for the robust and fully automable routine analysis of minute amounts of biological samples. Among the various chromatographic and mass spectrometric modes available in principle, ion-pair reversed-phase HPLC and electrospray ionization mass spectrometry (ESI-MS) have been shown to be the most suitable for the direct interfacing of liquid chromatography (LC) and MS. Instrumental setup, as well as chromatographic and mass spectrometric experimental conditions, need to be carefully selected in order to maximize the performance of the hyphenated analytical system. Applications of HPLC-ESI-MS include the characterization of oligodeoxynucleotides synthesized by solid-phase synthesis, the analysis of antisense oligodeoxynucleotides, oligonucleotide metabolites, and DNA adducts, the analysis of genomic segments specifically amplified by the polymerase chain reaction (PCR), the characterization of ribonucleic acids, the sizing of double-stranded DNA restriction fragments, the genotyping of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), the detection of mutations in nucleic acid sequences, and the sequencing of nucleic acids.

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Fragmentation reactions of all 64 protonated trimer oligodeoxynucleotides and 16 mixed base tetramer oligodeoxynucleotides via tandem mass spectrometry in an ion trap

Cited by 41 publications

References 29 publications

Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

A mechanistic study of the electron capture dissociation of oligonucleotides

Analysis of nucleic acids by on‐line liquid chromatography–Mass spectrometry

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