A correlation algorithm for the automated quantitative analysis of shotgun proteomics data
A correlation algorithm for the automated quantitative analysis of shotgun proteomics data
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DOI：
10.1021/ac034790h
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发表时间：
2003-12-15
影响因子：
7.4
通讯作者：
Yates, JR
中科院分区：
文献类型：
--
作者：
MacCoss, MJ;Wu, CC;Yates, JR
定量鸟枪蛋白质组学分析，促进使用化学标签，如ICAT和代谢标记策略与稳定同位素。快速高通量生产的定量“鸟枪”蛋白质组数据需要开发软件，自动转换成相对蛋白质丰度的肽质谱衍生数据。我们描述了一个计算机程序，称为RelEx，它使用最小二乘回归的肽离子电流比从质谱衍生的离子色谱图的计算。RelEx可容忍较差的信噪比数据，并可自动丢弃无用的色谱图和离群值比率。我们对系统误差进行了简单的校正，将定量测量的准确度提高了32 +/-4%。我们的自动化方法进行了验证，使用标记的混合物组成的已知的摩尔比，并证明了在一个真实的样品，通过测量渗透压对蛋白质表达的影响，在酿酒酵母。
Quantitative shotgun proteomic analyses are facilitated using chemical tags such as ICAT and metabolic labeling strategies with stable isotopes. The rapid high-throughput production of quantitative "shotgun" proteomic data necessitates the development of software to automatically convert mass spectrometry-derived data of peptides into relative protein abundances. We describe a computer program called RelEx, which uses a least-squares regression for the calculation of the peptide ion current ratios from the mass spectrometry-derived ion chromatograms. RelEx is tolerant of poor signal-to-noise data and can automatically discard nonusable chromatograms and outlier ratios. We apply a simple correction for systematic errors that improves the accuracy of the quantitative measurement by 32 +/- 4%. Our automated approach was validated using labeled mixtures composed of known molar ratios and demonstrated in a real sample by measuring the effect of osmotic stress on protein expression in Saccharomyces cerevisiae.