Traveling wave ion mobility (TWIM) mass spectrometry (MS) is a powerful method for the structural and conformational analysis of proteins and peptides, enabling the differentiation of isomeric peptides (or proteins) that have the same sequence but are modified at different residues. In this study, the TWIM‐MS technique was used to separate isomeric AuI metallopeptide ions that were formed by ZnII displacement from the parent zinc fingers (ZFs). The synthetic gold finger peptides were derived from the C‐terminus of the HIV nucleocapsid p7 protein (NCp7‐F2) and finger 3 of the Sp1 transcription factor (Sp1‐F3). TWIM‐MS enabled the acquisition of distinct product ion spectra for each isomer, clearly indicating the binding sites for the major conformers in the presence of multiple coordination possibilities. Collision cross‐section measurements showed that the aurated peptide has a slightly more compact structure than the parent zinc compound NCp7‐F2, which showed only one conformation. Goldrichtige Methode: Wanderwellen‐Ionenmobilitätsmassenspektrometrie wurde verwendet, um die Isomere von Gold(I)‐metallierten Peptidionen zu trennen, und ermöglichte so die Aufnahme unterschiedlicher Produktionenspektren für jedes Isomer (blau und rot). Die gemessenen Stoßquerschnitte zeigen, dass das Gold‐substituierte Peptid etwas kompakter als der ursprüngliche Zinkfinger ist.