Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

Area of Science:

• Proteomics
• Systems Biology
• Yeast Genetics

Background:

• Comprehensive proteome analysis presents significant challenges.
• Accurate relative quantification of endogenous proteins is crucial for understanding cellular function.

Purpose of the Study:

• To compare protein levels between haploid and diploid yeast cells.
• To demonstrate the capabilities of advanced computational proteomics and mass spectrometry.
• To investigate the proteomic basis of mating response and cell morphology differences.

Main Methods:

• Utilized Stable-Isotope Labeling by Amino acids in Cell culture (SILAC) for precise quantification.
• Employed advanced computational proteomics, instrument performance enhancements, and optimized sample preparation.
• Analyzed protein abundance across more than four orders of magnitude, including membrane and low-abundance proteins.

Main Results:

• Achieved accurate proteome-wide quantification, with most proteins showing one-to-one ratios between haploid and diploid cells.
• Identified specific proteins in haploid yeast, including key pheromone pathway members and retrotransposon-associated proteins.
• Observed significant changes in cell wall components, correlating with geometric differences between cell types.
• Found poor overall correlation between transcriptome and proteome, but good correlation for pheromone pathway components after data filtering.

Conclusions:

• Advanced proteomics enables comprehensive and precise quantification of cellular proteomes.
• Proteomic differences between haploid and diploid yeast provide insights into cell-specific functions and responses.
• Systems-wide protein quantification offers new perspectives for post-genomics and systems biology.