High resolution characterization of DNA fragment ions produced by ultraviolet matrix-assisted laser desorption/ionization using linear and reflecting time-of-flight mass spectrometry

Krause, Joern; Scalf, Mark; Smith, Lloyd M.

doi:10.1016/s1044-0305(99)00009-4

Cited by 13 publications

(14 citation statements)

References 19 publications

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“…Although many groups have reported the observation of different fragmentation in DE-reflecting and PSD spectra [22,26,28,29,32], we observed very few fragmentation pathways for both native and chargetagged forms of our 6-mers. The most likely reasons that our results differ from others are the choice of matrices and the sequences of the selected oligonucleotides.…”

Section: Discussioncontrasting

confidence: 62%

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

Chou

Limbach

Cole

2002

J. Am. Soc. Mass Spectrom.

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Section: Discussioncontrasting

confidence: 62%

“…These different experimental setups offered remarkably similar fragmentation patterns. Krause et al used MALDI-TOF-MS to investigate negative fragment ions to confirm their earlier hypothesis of the nucleobase protonation initiated fragmentation [32].…”

mentioning

confidence: 88%

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

Chou

Limbach

Cole

2002

J. Am. Soc. Mass Spectrom.

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“…Thus, the mass spectrometric behavior of oligonucleotides is usually studied in negative ion mode 1. The dissociation reactions of oligonucleotides at low excitation energies have been investigated by a number of laboratories using both collisional and radiative excitation in conjunction with quadrupole ion traps, FTICR, triple‐quadrupole and hybrid mass spectrometers 2–13. Base loss after deprotonation is suggested to be the dominating initial fragmentation step, often followed by a variety of different cleavages.…”

Section: Methodsmentioning

confidence: 99%

Characteristic fragmentation behavior of deoxytetranucleotides by positive ion electrospray ionization tandem mass spectrometry

Xiang

Abliz

et al. 2003

Rapid Comm Mass Spectrometry

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“…The dissociation of deprotonated ODNs has been extensively investigated by mass spectrometry (MS) coupled with soft ionization methods such as electrospray (ESI) and matrix-assisted laser desorption ionization (MALDI) [1][2][3][4][5][6][7][8][9][10][11][12][13][14]. It is known that the first step in the dissociation of deprotonated ODNs is loss of a nucleobase, either in a neutral (BH) or deprotonated (B Ϫ ) form [1,2,15].…”

mentioning

confidence: 99%

Investigation of the initial fragmentation of oligodeoxynucleotides in a quadrupole ion trap: Charge level-related base loss

Pan

Verhoeven

Lee

2005

J. Am. Soc. Mass Spectrom.

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The charge state distribution and CID fragmentation of two series of deprotonated oligodeoxynucleotide (ODN) 9-mers (5=-GGTTXTTGG-3= and 5=-CCAAYAACC-3=, X/Y ϭ G, C, A, or T) have been studied in detail in an ion trap in an effort to understand the intrinsic properties of DNA in vacuo. The distribution of charge states (Ϫ2 to Ϫ6) is similar for both the X-and Y-series, with the most abundant being the Ϫ4 charge state. The T-rich X-series prefers higher charge states (Ϫ6 and Ϫ5) than does the Y-series. Calculations show that phosphate groups located nearest a thymine are more acidic than those near an adenine, cytosine, or guanine, thus explaining why the X-series prefers higher charge states. We use the term "charge level" to define the ratio of the charge state to the total number of phosphate groups present in the ODN. We find, consistent with previous studies, that the initial step of fragmentation is loss of nucleobase either as an anion or as a neutral. We observe the former for ODNs with charge levels greater than 50% and the latter for ODNs with charge levels below 50%. The overall anionic base loss follows the trend A Ϫ Ͼ Ͼ G Ϫ Ϸ T Ϫ Ͼ C Ϫ ; electrostatic potential calculations indicate that this trend follows delocalization of electron density for each anion, with A Ϫ being the most stabilized through delocalization. For neutral base loss, thymine (TH) is rarely cleaved, while the preferences for AH, GH, and CH loss vary. Proton affinity (PA) calculations show that a nearby negatively charged phosphate enhances the PA of proximally located nucleobases; this PA enhancement probably plays a role in promoting neutral base loss. The trends differ by charge level. At a charge level of 37.5% (Ϫ3 charge state), AH loss is preferred over CH and GH loss, regardless of sequence. However, at a charge level of 25% (Ϫ2 charge state), the terminal bases are preferentially lost over the internal bases, regardless of identity. By reconstructing the ODN sequences from structurally informative (a-BH) and w ions, we are able to identify the charge locations for the Ϫ3 and Ϫ2 charge states. For the Ϫ3 charge state, one charge resides on each "most terminal" phosphate, with the third being in the middle. For the Ϫ2 charge state, each charge resides on the penultimate phosphate groups. We compare our data to earlier experiments in an effort to generalize trends. (J Am Soc Mass Spectrom 2005, 16, 1853-1865

show abstract

High resolution characterization of DNA fragment ions produced by ultraviolet matrix-assisted laser desorption/ionization using linear and reflecting time-of-flight mass spectrometry

Cited by 13 publications

References 19 publications

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

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

Characteristic fragmentation behavior of deoxytetranucleotides by positive ion electrospray ionization tandem mass spectrometry

Investigation of the initial fragmentation of oligodeoxynucleotides in a quadrupole ion trap: Charge level-related base loss

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