miRNA and DNA analysis by negative ion electron transfer dissociation and infrared multiple-photon dissociation mass spectrometry

• Published in: Analytica chimica acta Vol. 1299; p. 342431
• Main Authors: Guzmán-Lorite, Miriam, Rosu, Frédéric, Marina, María Luisa, García, María Concepción, Gabelica, Valérie
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 22.04.2024
• Subjects: DNA - genetics; Electrons; Fragmentation; microRNA; MicroRNAs; Oligonucleotide analysis; Spectrophotometry, Infrared; Tandem mass spectrometry; Tandem Mass Spectrometry - methods; Tandem mass spectrometry; Oligonucleotide analysis; microRNA; Fragmentation
• ISSN: 0003-2670; 1873-4324
• DOI: 10.1016/j.aca.2024.342431

The use of simple and hybrid fragmentation techniques for the identification of molecules in tandem mass spectrometry provides different and complementary information on the structure of molecules. Nevertheless, these techniques have not been as widely explored for oligonucleotides as for peptides or proteins. The analysis of microRNAs (miRNAs) warrants special attention, given their regulatory role and their relationship with several diseases. The application of different fragmentation techniques will be very interesting for their identification. Four synthetic miRNAs and a DNA sequence were fragmented in an ESI-FT-ICR mass spectrometer using both simple and hybrid fragmentation techniques: CID, nETD followed by CID, IRMPD, and, for the first time, nETD in combination with IRMPD. The main fragmentation channel was base loss. The use of nETD-IRMPD resulted in d/z, a/w, and c/y ions at higher intensities. Moreover, nETD-IRMPD provided high sequence coverage and low internal fragmentation. Native MS analysis revealed that only miR159 and the DNA sequence formed stable dimers under physiological ionic strength. The use of organic co-solvents or additives resulted in a lower sequence coverage due to lesser overall ionization efficiency. This work demonstrates that the combination of nETD and IRMPD for miRNA fragmentation constitutes a suitable alternative to common fragmentation methods. This strategy resulted in efficient fragmentation of [miRNA]5- using low irradiation times and fewer internal fragments while ensuring a high sequence coverage. Moreover, given that such low charge states predominate upon spraying in physiological-like conditions, native MS can be applied for obtaining structural information at the same time. [Display omitted] •Oligonucleotide fragmentation by nETD-IRMPD mainly produced c/y and d/z ions.•This technique resulted in low internal fragmentation and high sequence coverage.•MiR159 and DNA formed stable dimers under physiological conditions.•The use of solvents/additives for MS analysis of oligonucleotides reduces sequence coverage.