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


Mass spectrometry is a powerful technology for the analysis of large numbers of endogenous proteins1,2. However, the analytical challenges associated with comprehensive identification and relative quantification of cellular proteomes have so far appeared to be insurmountable3. 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) quantification4,5 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.

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Figure 1: Three strategies for in-depth quantification of the yeast proteome by SILAC labelling and high-resolution mass spectrometry.
Figure 2: Proteome coverage.
Figure 3: Quantitative differences between the haploid and diploid yeast proteome.
Figure 4: Proteome and transcriptome changes of haploid versus diploid yeast.


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G. de Souza measured part of the yeast proteome; C. Kumar contributed to bioinformatic analysis, G. Stoehr to proteome analysis. Z. Storchova provided the pGAL-HO plasmid. L.M.F.d.G. thanks D. Bertozzi for support and discussions. The Max-Planck Society and the DC-Thera and Interaction Proteome 6th framework projects of the European Union provided funding; T.C.W. is supported by the Human Frontier Science Program and M.L.N. by the European Molecular Biology Organization (EMBO).

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Correspondence to Tobias C. Walther or Matthias Mann.

Supplementary information

Supplementary Information

This file contains Supplementary Materials, Supplementary References, Supplementary Figures 1-10 with Legends, Supplementary Tables 5, 9, 10, and a description of columns in Excel sheets for proteome identification and quantitation for Supplementary Tables 1,2,3,4, and 6 (protein lists), Supplementary Table 7 (peptides list) and Supplementary Table 8 (KEGG and GO analysis). (PDF 11070 kb)

Supplementary Table 1

Supplementary Table 1: List of identified proteins for strategy a (trypsin experiment). (XLS 4904 kb)

Supplementary Table 2

Supplementary Table 2: List of identified proteins for strategy b (IEF-Full mass range MS - Lys-C experiment). (XLS 5339 kb)

Supplementary Table 3

Supplementary Table 3: List of identified proteins for strategy c (IEF-Narrow MS ranges - Lys-C experiments). (XLS 5048 kb)

Supplementary Table 4

Supplementary Table 4: List of identified proteins for strategies abc (trypsin and Lys-C experiment). (XLS 5924 kb)

Supplementary Table 6

Supplementary Table 6: Quantitative data for Lys-C experiment (proteins). (XLS 5435 kb)

Supplementary Table 7

Supplementary Table 7: Quantitative data for Lys-C experiment (peptides). (XLS 12183 kb)

Supplementary Table 8

Supplementary Table 8: Gene Ontology and Kegg pathway analysis of protein classes. (XLS 39 kb)

Supplementary Table 11

Supplementary Table 11: Gene Ontology and Kegg pathway analysis of protein classes. (XLS 35 kb)

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de Godoy, L., Olsen, J., Cox, J. et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251–1254 (2008).

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