Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.
Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.
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DOI：
10.1074/mcp.m112.023754
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发表时间：
2013-06
期刊：
影响因子：
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通讯作者：
Aebersold R
中科院分区：
文献类型：
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作者：
Gunaratne J;Schmidt A;Quandt A;Neo SP;Saraç OS;Gracia T;Loguercio S;Ahrné E;Xia RL;Tan KH;Lössner C;Bähler J;Beyer A;Blackstock W;Aebersold R
我们报告了一个高质量和系统范围的蛋白质组目录，涵盖了裂殖酵母裂殖酵母的预测基因的71%（3，542种蛋白质），为这个重要的模式生物提供了迄今为止最大的蛋白质数据集。我们获得了这种高蛋白质组和肽（11.4肽/蛋白质）的覆盖范围，通过广泛的样品分馏，高分辨率Orbitrap质谱，并结合数据库搜索使用iProphet软件作为跨蛋白质组学管道的一部分。所有原始数据和处理后的数据都可以在S. pombe PeptideAtlas.鉴定的蛋白质在功能特性上没有偏差，并允许对蛋白质丰度进行全局估计。PeptideAtlas的高覆盖率允许以系统范围的方式与转录组学数据相关，表明转录后过程控制所有鉴定的蛋白质中至少一半的水平。有趣的是，对于所有功能类别，相关性并不同样紧密，范围从参与翻译的蛋白质的rs >0.80到信号转导蛋白质的rs <0.45。此外，许多参与DNA损伤修复的蛋白质在PeptideAtlas中无法检测到，尽管它们的mRNA水平很高，这加强了这类蛋白质成员的按需免疫假说。总之，广泛的和公开可用的S。pombe PeptideAtlas与所产生的蛋白质型肽谱库一起将是对该微生物进行未来有针对性的、深入的和定量的蛋白质组学研究的有用资源。
We report a high quality and system-wide proteome catalogue covering 71% (3,542 proteins) of the predicted genes of fission yeast, Schizosaccharomyces pombe, presenting the largest protein dataset to date for this important model organism. We obtained this high proteome and peptide (11.4 peptides/protein) coverage by a combination of extensive sample fractionation, high resolution Orbitrap mass spectrometry, and combined database searching using the iProphet software as part of the Trans-Proteomics Pipeline. All raw and processed data are made accessible in the S. pombe PeptideAtlas. The identified proteins showed no biases in functional properties and allowed global estimation of protein abundances. The high coverage of the PeptideAtlas allowed correlation with transcriptomic data in a system-wide manner indicating that post-transcriptional processes control the levels of at least half of all identified proteins. Interestingly, the correlation was not equally tight for all functional categories ranging from rs >0.80 for proteins involved in translation to rs <0.45 for signal transduction proteins. Moreover, many proteins involved in DNA damage repair could not be detected in the PeptideAtlas despite their high mRNA levels, strengthening the translation-on-demand hypothesis for members of this protein class. In summary, the extensive and publicly available S. pombe PeptideAtlas together with the generated proteotypic peptide spectral library will be a useful resource for future targeted, in-depth, and quantitative proteomic studies on this microorganism.