Fast ATOM Bombardment Mass Spectra of Nucleosides. Comparison with Electron Impact and Chemical Ionization Mass Spectra

Accurate Quantification of Ten Methylated Purine Nucleosides by Highly Sensitive and Stable Isotope-Diluted UHPLC-MS/MS

The dynamic landscape of cellular nucleotides/nucleosides associated with RNA metabolism, particularly in diseases like cancer, has spurred intensive interest. Here, we report a robust stable isotope-diluted UHPLC-ESI-MS/MS method for accurate quantification of 12 purine ribonucleosides, including 10 methylated purine nucleosides. By the use of thermally decomposable ammonium bicarbonate (NH4HCO3) as a mobile phase additive for UHPLC-MS/MS detection, the ESI-MS/MS signal responses of these target compounds were enhanced by 1.7-24.5 folds. Noteworthily, three methylated guanosine isomers (m1G, m2G, and m7G) and two methylated adenosine isomers (m1A and m6A) that are indistinguishable directly by mass spectrometry were well resolved with optimal UHPLC separation. Combined with methanol extraction and solid-phase extraction (SPE) pretreatment, the method quantified intracellular concentrations of three modified nucleosides (Gm, m1G, and m2G), which would otherwise be undetectable because of significant suppression of their signals by the interfering cellular matrix. Nine purine nucleosides were simultaneously quantified in 293T cells, and their concentrations ranged by 4 orders of magnitude. Overall, the method presents high recovery rates over 90% for endogenous modified purine nucleosides in cultured cells, along with good precision, linearity, and LOD ranging from 0.30 fmol to 0.37 pmol per 5 × 105 cells. The developed UHPLC-MS/MS method holds potential for screening purine nucleosides as diagnostic and prognostic biomarkers and for quantifying purine epigenetic nucleosides post-cell metabolome analysis, thereby providing a valuable analytical tool for intracellular nucleoside quantification in future clinical research.

Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code

The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.

Mass spectrometry analysis of nucleosides and nucleotides

Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.

Mass spectrometry in the biology of RNA and its modifications

Many powerful analytical techniques for investigation of nucleic acids exist in the average modern molecular biology lab. The current review will focus on questions in RNA biology that have been answered by the use of mass spectrometry, which means that new biological information is the purpose and outcome of most of the studies we refer to. The review begins with a brief account of the subject "MS in the biology of RNA" and an overview of the prevalent RNA modifications identified to date. Fundamental considerations about mass spectrometric analysis of RNA are presented with the aim of detailing the analytical possibilities and challenges relating to the unique chemical nature of nucleic acids. The main biological topics covered are RNA modifications and the enzymes that perform the modifications. Modifications of RNA are essential in biology, and it is a field where mass spectrometry clearly adds knowledge of biological importance compared to traditional methods used in nucleic acid research. The biological applications are divided into analyses exclusively performed at the building block (mainly nucleoside) level and investigations involving mass spectrometry at the oligonucleotide level. We conclude the review discussing aspects of RNA identification and quantifications, which are upcoming fields for MS in RNA research. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.

Structural characterization of modified nucleosides in tRNA hydrolysates by frit-fast atom bombardment liquid chromatography/mass spectrometry

Feasibility for the structural characterization of modified nucleosides in transfer RNA at low microgram levels has been investigated by using continuous-flow frit-fast atom bombardment liquid chromatography/mass spectrometry (frit-FAB LC/MS). Sample of tRNA(Phe) from brewer's yeast (Saccharomyces cerevisiae) was used as a main model, and enzymatically hydrolysed by nuclease P1 and alkaline phosphatase. The resulting nucleoside mixture was separated by using a microbore reversed-phase LC column (150 mm x 0.5 mm i.d.) with an aqueous ammonium acetate-methanol gradient, and the mass spectra were acquired on both positive and negative ionization modes. The modified nucleosides were characterized by comparison of the relative LC elution times with authentic nucleosides, and further confirmed by the structural information from the frit-FAB mass spectra where both molecular and base ions were in general observed as intense peaks in both ionization modes. Typically, 0.06-0.2 A260 units (3-10 micrograms) of isoaccepting tRNA was enough to obtain full-scan mass spectra of modified nucleosides, often occurring at a frequency of one per tRNA molecule using positive ion detection. The LC/MS system was used to screen modified nucleosides in tRNA of the extremely thermophilic microorganism Pyrodictium occultum.

Detection and structural characterization of amino polyaromatic hydrocarbon-deoxynucleoside adducts using fast atom bombardment and tandem mass spectrometry

Fast atom bombardment (FAB) and tandem mass spectrometry (MS/MS) are shown to be useful methods for the detection and structural characterization of nanogram amounts of amino polyaromatic hydrocarbon-nucleoside DNA adducts. The positive ion spectra of four aromatic amine guanosine adducts were studied in detail. The FAB spectra of these adducts exhibit an [MH]+ ion and a more abundant aglycon fragment ion, [AH2]+, which results from the loss of the deoxyribose sugar. The sensitivity of the adducts to FAB was enhanced by preparing trimethylsilyl (TMS) ether derivatives. High-quality full-scan spectra could be obtained on less than 70 ng of the derivatized adducts without signal averaging. With a B/E-linked scan of the [MH]+ ion for the TMS2 species, these same adducts could be detected by examination of their metastable ion spectra at levels as low as 4-5 ng (S/N greater than 10). Collision-induced dissociation (CID) of the [MH]+ ion yields the aglycon fragment and an ion, S1, which results from cleavage through the sugar. The CID spectrum of the aglycon [AH2]+ ion is much more useful, providing structural information relating to the base, the polyaromatic hydrocarbon, and, possibly, the site of covalent attachment. Differentiation of isomeric aminophenanthrene-guanine adducts was demonstrated on the basis of the CID spectra of their respective [AH2]+ ions. The use of TMS derivatives also improves the sensitivity of these methods.

Mass spectrometry of electrophore-labeled nucleosides. Pentafluorobenzyl and cinnamoyl derivatives

Three structurally similar deoxynucleosides (thymidine, O4-ethylthymidine, and 2'-deoxyuridine) were studied by mass spectrometry as pentafluorobenzyl, cinnamyl, or mixed derivatives. The purpose of the work was to define the usefulness of such derivatives for structural elucidation of deoxynucleosides. The compounds were ionized in three ways: electron capture negative ion, positive ion chemical ionization, and electron impact. For each of the derivatives examined, the combined spectra were well suited for structural elucidation purposes.

Self-chemical ionization Fourier transform ion cyclotron resonance mass spectrometry: identification and characterization of modified and unmodified bases and nucleosides

Self-chemical ionization Fourier transform ion cyclotron resonance (FT-ICR) mass spectra are reported for bases, nucleosides, and alkylated and exocyclic adducts of bases and nucleosides. The technique always produces a protonated molecular ion and in the majority of cases this is a single, intense peak. Analysis of a base mixture and a nucleoside mixture demonstrates the technique as an excellent method to identify the constituent compounds qualitatively. The high resolution capabilities and tandem mass spectrometric techniques (msn) in FT-ICR are discussed with respect to developing the technique as a future method to identify and characterize nucleic acid constituents, specifically adducts.