Factors influencing oligonucleotide stability in matrix-assisted laser desorption/ionization (MALDI) mass spectroscopy

Tang, Wei; Krause, Joern; Zhu, Lin; Smith, Lloyd M.

doi:10.1016/s0168-1176(97)00204-8

Cited by 19 publications

(8 citation statements)

References 17 publications

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“…Metastable decay of pre‐selected precursor ions in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐ToF‐MS) is a powerful tool for the identification and sequencing of proteins 1–3. At the same time, however, the metastable and prompt decay in MALDI when acquiring mass spectra of oligonucleotides may become a major obstacle 4–9. Furthermore, the strong affinity of oligonucleotides to form sodium adducts complicates the sample preparation considerably and often sets limits to the achievable resolution 4.…”

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confidence: 99%

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Effective quenching of fragment formation in negative ion oligonucleotide matrix‐assisted laser desorption/ionization mass spectrometry through sodium adduct formation

Staňo

Flosadóttir

Ingólfsson

2006

Rapid Comm Mass Spectrometry

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Metastable decay of the sodium-free and the sodium adducts of the negatively charged hexameric nucleotides 5'-d(TTXYTT)-3' (X and Y are dC, dG or dA) in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS) is reported. We show that the sodium adduct formation may be used to quantitatively quench dissociation channels in oligonucleotide MALDI-MS, and we argue, that by means of effective steps in the sample preparation that lead to per-sodiation of the sample, the sample preparation and the mass resolution of oligonucleotide mass spectra in MALDI may be improved substantially. The dependency of the fragment formation on the degree of sodiation is also discussed in context with the underlying fragmentation mechanisms.

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confidence: 99%

“…There has been substantial effort to understand the fragmentation mechanism behind the prompt and metastable decay of oligonucleotides in MALDI 4–7, 9, 23–32. Much of this work was reviewed by Wan and Gross in 2001 and by Wu and McLuckey in 2004 6, 32.…”

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confidence: 99%

Effective quenching of fragment formation in negative ion oligonucleotide matrix‐assisted laser desorption/ionization mass spectrometry through sodium adduct formation

Staňo

Flosadóttir

Ingólfsson

2006

Rapid Comm Mass Spectrometry

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“…18 The higher stability of the N-glycosidic bond of thymidine versus other nucleosides has already been observed in MALDI-MS of nucleic acids. 19 Thymidine has the lowest proton affinity of the nucleosides and is less prone to fragmentation.…”

Section: Resultsmentioning

confidence: 89%

Analysis of solid-supported oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Meyer

Spinelli

Imbach

et al. 2000

Rapid Commun. Mass Spectrom.

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This study presents matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) as a powerful tool to analyze and characterize oligonucleotides covalently linked to a solid support during their synthesis. The analysis of the fragment ions generated either in negative or positive mode allows direct and easy access to the nucleotide sequence and identification of the internucleosidic linkage. The mechanisms of the fragmentation of the solid-supported oligonucleotides induced by MALDI-TOFMS are discussed. Copyright 2000 John Wiley & Sons, Ltd.

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“…Furthermore, delayed extraction technology has been used to examine in‐source fragmentation observed in the same spectrum as the parent ion 14–17. Of the many matrices for DNA, 2,5‐dihydroxybenzoic acid (2,5‐DHB)18–21 is frequently used because both in‐source fragment ions and parent ions are observed with signal‐to‐noise ratios (S/N) high enough to perform accurate mass measurements 22–24. In addition to the matrix, ammonium matrix additives are necessary to discourage alkali metal adduction, aid in the co‐crystallization of the DNA with the matrix and control fragmentation so that sufficient signals for DNA ions can be obtained 26.…”

Section: Introductionmentioning

confidence: 99%

Ultraviolet/matrix-assisted laser desorption/ionization mass spectrometric characterization of 2,5-dihydroxybenzoic acid-induced reductive hydrogenation of oligonucleotides on cytosine residues

Koomen

Russell

2000

J. Mass Spectrom.

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The changes in the ion signals in the isotope cluster, mass resolution, signal-to-noise ratio and mass accuracy for matrix-assisted laser desorption/ionization (MALDI) of DNA oligonucleotides (dGGATC, dCAGCt, and dAACCGTT) and their fragment ions were evaluated, and these data were compared with those obtained using 3-hydroxypicolinic acid. Mass spectra obtained by using 2,5-dihydroxybenzoic acid (2,5-DHB) appear to have differences from the theoretical isotopic clusters, which arise by reductive hydrogenation producing a second peak at the M + 2 isotope of the native oligonucleotide. Based on the patterns of the isotopic envelope observed in the in-source decay fragments, we propose that cytosine is the site of reduction. We do not find evidence of reduction of oligonucleotides, viz. dTGGGGTT, that do not contain cytosine; however, 2'-deoxycytidine and 2'-deoxycytidine-5'-monophosphate undergo reductive hydrogenation. Several experiments were carried out in an effort to determine whether the reductive hydrogenation occurs during sample preparation or as a result of laser irradiation. The results of these experiments suggest that it occurs during sample preparation. The relative intensities of ion signals corresponding to the reduced base can be altered by using different matrix additives (aminonaphthalenes) or a different substrate (copper). Also, the oxidized form of 2,5-DHB is trapped by reaction with the side chain of cysteine in glutathione, providing evidence that the reaction occurs in solution as the matrix crystallizes.

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Factors influencing oligonucleotide stability in matrix-assisted laser desorption/ionization (MALDI) mass spectroscopy

Cited by 19 publications

References 17 publications

Effective quenching of fragment formation in negative ion oligonucleotide matrix‐assisted laser desorption/ionization mass spectrometry through sodium adduct formation

Effective quenching of fragment formation in negative ion oligonucleotide matrix‐assisted laser desorption/ionization mass spectrometry through sodium adduct formation

Analysis of solid-supported oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Ultraviolet/matrix-assisted laser desorption/ionization mass spectrometric characterization of 2,5-dihydroxybenzoic acid-induced reductive hydrogenation of oligonucleotides on cytosine residues

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