Motivation: Labelling experiments in biology usually make use of isotopically-enriched substrates, with the two most commonly employed isotopes for metabolism being 2 H and 13 C. At the end of the experiment some metabolites will have incorporated the labelling isotope, to a degree that depends on the metabolic turnover. In order to propose a meaningful biological interpretation, it is necessary to estimate the amount of labelling, and one possible route is to exploit the fact that MS isotopic patterns reflect the isotopic distributions. Results: We developed the IsotopicLabelling R package, a tool able to extract and analyse isotopic patterns from liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-MS (GC-MS) data relative to labelling experiments. This package estimates the isotopic abundance of the employed stable isotope (either 2 H or 13 C) within a specified list of analytes. Availability: The IsotopicLabelling R package is freely available at https://github.com/RuggeroFerrazza/IsotopicLabelling