With all the power of modern mass spectrometry (MS) that made it a dominant analytical approach, characterizing complex and particularly isomeric mixtures requires prior separations. Ion mobility spectrometry (IMS) is a competitor to chromatography and electrophoresis, providing faster and often more specific results. In particular, differential IMS (FAIMS) is highly orthogonal to MS and thus capable of fine isomeric resolution. Previously, FAIMS has distinguished isotopomers of single amino acids differing in the heavy atom position. Here we extend such isotopomer separations to larger species – the protonated synthetic di- and trialanines with one labeled residue. Small isotopic shifts are accurately quantified employing the unlabeled analogs as internal calibrants. The effect is measured as a function of dispersion field and buffer gas composition, especially in the He/N2 and He/CO2 mixtures that broadly improve FAIMS performance. Full separation of dialanine isotopomers and partial resolution of trialanine isotopomers have been achieved under optimum conditions.