A comparative NAIL-MS experiment is quite similar to a SILAC experiment but for RNA instead of proteins. First, two populations of the respective cells are cultivated. One of the cell populations is fed with growth medium containing unlabeled nutrients, whereas the second population is fed with growth medium containing stable isotope labeled nutrients. The cells then incorporate the respective isotopologues into their RNA molecules. One of the cell populations serves as a control group whereas the other is subject to the associated research (e.g. KO strain, stress). Upon harvesting of the two cell populations they are mixed and co-processed together to exclude purification-bias. Due to the distinct masses of incorporated nutrients into the nucleosides a differentiation of the two cell populations is possible by mass spectrometry.