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

Anal Chim Acta. 2024 Apr 22;1299:342431. doi: 10.1016/j.aca.2024.342431. Epub 2024 Feb 27.ABSTRACTBACKGROUND: 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.RESULTS: 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.NOVELTY: This work demonstrates that the combination of nETD and IRMPD for miRNA fragmentation constitutes a suitable alternative ...

Source: Analytica Chimica Acta - March 18, 2024 Category: Chemistry Authors: Miriam Guzm án-Lorite Fr édéric Rosu Mar ía Luisa Marina Mar ía Concepción García Val érie Gabelica Source Type: research