Methyl-SILAF mapping of the Drosophila mitochondrial protein methylome

S-adenosylmethionine (SAM) is the principal biological methyl group donor for a diverse range of substrates. It is synthesised in the cytosolic methionine cycle and shuttled throughout the cell. The mitochondrial SAM (mitoSAM) pool depends on import through the inner-membrane S-adenosylmethionine carrier (SAMC) and supports the maturation of metabolites and mitochondrial RNAs. Mutations in SAMC in patients cause a severe metabolic crisis, however, the organellar regulation of mitoSAM and the protein methylation landscape within mitochondria are largely unknown. We developed a fly-compatible SILAC labelling technique and mapped mitochondrial protein methylation sites in Drosophila melanogaster, further showing that SAM is the sole methyl group donor for these modifications, with no contribution from folate-species. This dataset comprises MS-runs used for quality control of methyl-SILAF, the methylome mapping and exclusion of folates as protein methyl-group donors.