High‐resolution ion mobility spectrometry‐mass spectrometry of isomeric/isobaric ribonucleotide variants

Abstract

In this report, we explored the benefits of cyclic ion mobility (cIM) mass spectrometry in the analysis of isomeric post‐transcriptional modifications of RNA. Standard methyl‐cytidine samples were initially utilized to test the ability to correctly distinguish different structures sharing the same elemental composition and thus molecular mass. Analyzed individually, the analytes displayed characteristic arrival times (tD) determined by the different positions of the modifying methyl groups onto the common cytidine scaffold. Analyzed in mixture, the widths of the respective signals resulted in significant overlap that initially prevented their resolution on the tD scale. The separation of the four isomers was achieved by increasing the number of passes through the cIM device, which enabled to fully differentiate the characteristic ion mobility behaviors associated with very subtle structural variations. The placement of the cIM device between the mass‐selective quadrupole and the time‐of‐flight analyzer allowed us to perform gas‐phase activation of each of these ion populations, which had been first isolated according to a common mass‐to‐charge ratio and then separated on the basis of different ion mobility behaviors. The observed fragmentation patterns confirmed the structures of the various isomers thus substantiating the benefits of complementing unique tD information with specific fragmentation data to reach more stringent analyte identification. These capabilities were further tested by analyzing natural mono‐nucleotide mixtures obtained by exonuclease digestion of total RNA extracts. In particular, the combination of cIM separation and post‐mobility dissociation allowed us to establish the composition of methyl‐cytidine and methyl‐adenine components present in the entire transcriptome of HeLa cells. For this reason, we expect that this technique will benefit not only epitranscriptomic studies requiring the determination of identity and expression levels of RNA modifications, but also metabolomics investigations involving the analysis of natural extracts that may possibly contain subsets of isomeric/isobaric species.

Combination of IM-Based Approaches to Unravel the Coexistence of Two Conformers on a Therapeutic Multispecific mAb

“…This design affords higher resolving power through multipass separation, and also offers the unique opportunity to perform IM n experiments to further explore mobility-separated populations. 21 The cIM-MS platform has proved particularly useful in several studies to differentiate small isomeric analytes, 22 , 23 with up to R ∼ 750 Ω/ΔΩ obtained after 100 passes. 21 On the other hand, only few papers have reported the use of high-resolution cIM-MS for the analysis of larger biomolecules (proteins).…”

Advancements in the characterisation of oligonucleotides by high performance liquid chromatography‐mass spectrometry in 2021: A short review

“…Recently, ion mobility spectrometry (IMS) has been used, in conjunction to CID, for the separation of different lengths, identification of w and y fragments 23 but also to separate different charges, 24 separate nucleotides, and nucleosides, 25 separate folded and unfolded oligonucleotides and isobaric ions. 26 Furthermore, hydrophilic interaction chromatography (HILIC) 27 and two-dimensional liquid chromatography (2D-LC) 28 have been used as an alternative to IP-RPLC. 29 This review covers the different advancements for the analysis…”

Cyclic Ion Mobility Spectrometry Coupled to High-Resolution Time-of-Flight Mass Spectrometry Equipped with Atmospheric Solid Analysis Probe for the Molecular Characterization of Combustion Particulate Matter

“…Aside from a higher resolving power, a higher number of data points (bins) are beneficial for an accurate description of the IMS-profile of complex isomeric mixtures. − A very recent technology is cyclic ion mobility spectrometry (cIMS), allowing for the ions to pass multiple times in a circular traveling wave array, increasing the IMS resolving power by a factor of the square root of the pass number. In combination with an ion storage device before and after the cyclic array as well as with an option for collision-induced dissociation (CID), enormous flexibility is enabled for detailed molecular description.…”