Stable isotope labeling of amino acids in cell culture (SILAC) combined with liquid chromatography—tandem mass spectrometry (MS) was used to obtain quantitative information for approximately 70–80% of all verified open reading frames (ORFs) in disomic strains relative to wild-type cells. This comprehensive approach provides global measurement of proteome changes across 12 different aneuploid yeast strains. [@dephoure_quantitative_2014]
Definitions
- liquid chromatography—tandem mass spectrometry
- open reading frames
- disomic strains
- proteome
- protein abundance
- aneuploid yeast
- silac
- wild-type cells
Synthesis
Quantitative proteomics using liquid chromatography-tandem mass spectrometry successfully measures 70-80% of yeast open reading frames, providing comprehensive coverage of the proteome to assess protein abundance across different strains. This high-coverage methodology has proven particularly valuable for studying aneuploid yeast, where it reveals that proteins encoded by duplicated chromosomes increase approximately twofold in abundance, demonstrating that protein stoichiometry tracks gene dosage with high fidelity when chromosomal position is considered. However, the proteome composition measured in these studies may be significantly influenced by growth medium conditions, as different experimental approaches employ distinct media—synthetic medium for SILAC versus rich YEPD medium for TMT analysis—raising unresolved questions about how medium-dependent effects might impact the observed protein abundance patterns in disomic strains compared to wild-type cells.
Related
- Growth medium conditions affect aneuploid strain proteome composition
- Aneuploidy alters cellular protein composition approximately twofold
- Protein levels correlate with chromosomal position in aneuploid strains