You can add or edit labelling schemes by going to Molecule and selecting Isotopomer Schemes (version 2.1) or Reference Isotope Schemes (version 2.2 onwards). Either click New to create a new labelling scheme, or select a scheme you wish to alter and click Copy. In the Isotopomers tab you can specify each isotopomer and the way in which the atoms in that isotopomer are labelled. In the top half of the pop-up you will see all the isotopomers and you can add or delete them using the buttons below the list. Add Default Abundance Set will add a set of 20 amino acids using the Default Abundance. By default this is the natural abundance. If you wish, you can change the Default Abundance using the Set Default Abundances button above the list of isotopomers. This is useful if all amino acids have the same labelling. In the lower part of the pop-up you will see the labelling at each atomic site for the isotopomer selected above. Here you can change the weighting of different isotopes to create the correct degree of labelling if this is specific to certain sites. Unlabelled sites should on the whole be set to natural abundance levels rather than 0.