NAIL-MS is used to study RNA modification mechanisms. Therefore, cells in culture are first fed with stable isotope labeled nutrients and the cells incorporate these into their biomolecules. After purification of the nucleic acids, most often RNA, analysis is done by mass spectrometry. Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of ions. Pairs of chemically identical nucleosides of different stable-isotope composition can be differentiated in a mass spectrometer due to their mass difference. Unlabeled nucleosides can therefore be distinguished from their stable isotope labeled isotopologues. For most NAIL-MS approaches it is crucial that the labeled nucleosides are more than 2 Da heavier than the unlabeled ones. This is because 1.1% of naturally occurring carbon atoms are C isotopes. In the case of nucleosides this leads to a mass increase of 1 Da in ~10% of the nucleosides. This signal would disturb the final evaluation of the measurement.
NAIL-MS can be used to investigate RNA modification dynamics by changing the labeled nutrients of the corresponding growth medium during the experiment. Furthermore, cell populations can be compared directly with each other without effects of purification bias. Furthermore, it can be used for the production of biosynthetic isotopologues of most nucleosides which are needed for quantification by mass spectrometry and even for the discovery of yet unknown RNA modifications.