In general, cells are cultivated in unlabeled or stable (non-radioactive) isotope labeled media. For example, the medium can contain glucose labeled with six carbon-13 atoms (13C) instead of the normal carbon-12 (12C). Cells growing in this medium, will, depending on model organism, incorporate the heavy glucose into all of their RNA molecules. Thereafter, all nucleotides are 5 Da heavier than their unlabeled isotopologues due to a complete carbon labeling of the ribose. After cultivation and appropriate labeling of the cells, they are generally harvested using phenol/chloroform/guanidinium isothiocyanate. Other extraction methods are possible and sometimes needed (e.g. for yeast). RNA is then isolated by Phenol-Chloroform extraction and iso-Propanol precipitation. Further purification of specific RNA species (e.g. rRNA, tRNA) is usually done by size-exclusion chromatography (SEC) but other approaches are available as well. For most applications the final product needs to be enzymatically digested to nucleosides before analysis by LC-MS. Therefore, digestion enzymes such as benzonase, NP1 and CIP are used. Typically, a triple quadrupole in MRM mode is used for the measurements.
