Fragmentation mechanisms of oligonucleotides in MALDI mass spectrometry

Christine M. Nelson; Lin Zhu; Wei Tang; Lloyd M. Smith; Kevin Crellin; Jamal Berry; Jack L. Beauchamp

doi:10.1117/12.237612

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1 April 1996 Fragmentation mechanisms of oligonucleotides in MALDI mass spectrometry

Christine M. Nelson, Lin Zhu, Wei Tang, Lloyd M. Smith, Kevin Crellin, Jamal Berry, Jack L. Beauchamp

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Proceedings Volume 2680, Ultrasensitive Biochemical Diagnostics; (1996) https://doi.org/10.1117/12.237612
Event: Photonics West '96, 1996, San Jose, CA, United States

Abstract

Early matrix assisted laser desorption/ionization (MALDI) studies of oligonucleotides elucidated many issues inherent to the analysis of nucleic acids. These studies demonstrated that fragmentation is an important issue and is responsible for some of the current limitations associated with the technique. Results in our laboratory and in others confirm that fragmentation is dependent on both oligonucleotide sequence and matrix composition. The proposed fragmentation pathway consists of nucleobase protonation inducing base loss followed by backbone cleavage at the 3' C-O bond on the corresponding deoxyribose. Using theoretical calculations, we explain why the four nucleobases display different fragmentation propensities. Additionally, if nucleobase protonation initiates fragmentation, then differences in fragmentation amounts when different matrices are used must be related to the various matrices' abilities to protonate the nucleobase. Currently, we are investigating the relationship between fragmentation propensity and matrix properties. Proton affinities of five common MALDI matrices have been measured and compared to fragmentation probabilities. By deepening our understanding of the fundamental chemistry of DNA fragmentation, we hope to be able to develop the MALDI technique into a powerful robust and versatile methodology for nucleic acid analysis.

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Christine M. Nelson, Lin Zhu, Wei Tang, Lloyd M. Smith, Kevin Crellin, Jamal Berry, and Jack L. Beauchamp "Fragmentation mechanisms of oligonucleotides in MALDI mass spectrometry", Proc. SPIE 2680, Ultrasensitive Biochemical Diagnostics, (1 April 1996); https://doi.org/10.1117/12.237612

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