Updated project metadata. Mitochondria derived from Saccharomyces cerevisiae grown on either a non-fermentable (glycerol) or a fermentable (glucose) carbon source were cross-linked with BS3. Additionally, by using a stable-isotope labelled quantitative cross-linking approach, we were able to quantify differences in protein-protein cross-links in mitochondria according to the growth condition. Furthermore, so far uncharacterized yeast proteins were put into biological context based on their cross-linking pattern.