一项将高分辨率质谱、“SILAC”标记和计算蛋白组学方法结合起来的研究工作，被用来实现蛋白组学中的一个重要目标：一个蛋白组的完全识别和量化。该研究发现了一个由多达4,399单个内生蛋白组成的蛋白组，就在正常生长的酵母细胞中所表达的蛋白而言，这实质上是一个完整的蛋白组。
研究人员将单倍体细胞中这些蛋白的水平与双倍体细胞中它们的水平进行了对比。除了其他差别之外，双倍体中细胞壁成分的含量也显著降低，这与双倍体比单倍体大两倍、但并没有两倍大的表面积这一事实是一致的。（生物谷Bioon.com）
生物谷推荐原始出处：
Nature 455, 1251-1254 (30 October 2008) | doi:10.1038/nature07341
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
Lyris M. F. de Godoy1,3, Jesper V. Olsen1,3, Jürgen Cox1,3, Michael L. Nielsen1,3, Nina C. Hubner1, Florian Fr?hlich2, Tobias C. Walther2 & Matthias Mann1
1 Proteomics and Signal Transduction, and,
2 Organelle Architecture and Dynamics, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
3 These authors contributed equally to this work.
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.
