Mass spec compatible yeast extract

To generate complex proteome samples with known composition a tryptic HeLa protein digest (Pierce™ HeLa Protein Digest Standard, Thermo Fisher Scientific, Dreieich, Germany), a tryptic yeast protein digest (Mass Spec-Compatible Yeast Extract, Promega, Walldorf, Germany) and an Escherichia coli (E. coli) tryptic protein digest (Waters, Manchester, UK) were used. For differential proteomics, three proteome mixtures (A, B, C) were prepared, composed of the HeLa proteome, yeast proteome, and E. coli proteome. A) 20 µg of HeLa digest (dissolved in 0.1% FA) was combined with 10 µg yeast digest (dissolved in 0.1% FA) and 2 µg E. coli digest (dissolved in 0.1% FA). B) 10 µg of HeLa digest (dissolved in 0.1% FA) was combined with 20 µg yeast digest (dissolved in 0.1% FA) and 2 µg E. coli digest (dissolved in 0.1% FA). C) 2 µg of HeLa digest (dissolved in 0.1% FA) was combined with 10 µg yeast digest (dissolved in 0.1% FA) and 20 µg E. coli digest (dissolved in 0.1% FA). The sample mixtures A, B and C had a final concentration of 2 µg µL -1 (dissolved in 0.1% FA).