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

• Published in: Nature Vol. 455; no. 7217; pp. 1251 - 1254
• Main Authors: de Godoy, Lyris M.F, Olsen, Jesper V, Cox, Jurgen, Nielsen, Michael L, Hubner, Nina C, Frohlich, Florian, Walther, Tobias C, Mann, Matthias
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.10.2008; Nature Publishing; Nature Publishing Group
• Subjects: Amino acids; arginine; Biological and medical sciences; carbon; Diploidy; Diverse techniques; Experiments; Fundamental and applied biological sciences. Psychology; fungal proteins; Gene Expression Profiling; Genes, Fungal - genetics; Haploidy; Humanities and Social Sciences; Identification; isotope labeling; Kinases; letter; lysine; Mass spectrometry; Mass Spectrometry - methods; Molecular and cellular biology; multidisciplinary; nitrogen; Oligonucleotide Array Sequence Analysis; Open Reading Frames; Proteins; proteome; Proteome - analysis; Proteome - genetics; Proteomics; Proteomics - methods; Retroelements - genetics; RNA, Fungal - analysis; RNA, Fungal - genetics; Saccharomyces cerevisiae; Saccharomyces cerevisiae - cytology; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - analysis; Saccharomyces cerevisiae Proteins - genetics; Sample preparation; Science; Science (multidisciplinary); Signal transduction; stable isotope labelling by amino acids; stable isotopes; Staining and Labeling; Transcription, Genetic - genetics; Yeasts; Ascomycota; Fungi; Haploidy; Diploidy; Yeast; Proteome; Bioinformatics; Saccharomyces cerevisiae; Mass spectrometry; Comparative study
• ISSN: 0028-0836; 1476-4687; 1476-4679
• DOI: 10.1038/nature07341

Mass spectrometry is a powerful technology for the analysis of large numbers of endogenous proteins. However, the analytical challenges associated with comprehensive identification and relative quantification of cellular proteomes have so far appeared to be insurmountable. Here, using advances in computational proteomics, instrument performance and sample preparation strategies, we compare protein levels of essentially all endogenous proteins in haploid yeast cells to their diploid counterparts. Our analysis spans more than four orders of magnitude in protein abundance with no discrimination against membrane or low level regulatory proteins. Stable-isotope labelling by amino acids in cell culture (SILAC) quantification was very accurate across the proteome, as demonstrated by one-to-one ratios of most yeast proteins. Key members of the pheromone pathway were specific to haploid yeast but others were unaltered, suggesting an efficient control mechanism of the mating response. Several retrotransposon-associated proteins were specific to haploid yeast. Gene ontology analysis pinpointed a significant change for cell wall components in agreement with geometrical considerations: diploid cells have twice the volume but not twice the surface area of haploid cells. Transcriptome levels agreed poorly with proteome changes overall. However, after filtering out low confidence microarray measurements, messenger RNA changes and SILAC ratios correlated very well for pheromone pathway components. Systems-wide, precise quantification directly at the protein level opens up new perspectives in post-genomics and systems biology.