Statistical identification of differentially labeled peptides from liquid chromatography tandem mass spectrometry
Statistical identification of differentially labeled peptides from liquid chromatography tandem mass spectrometry
复制标题
DOI：
10.1002/pmic.200601034
复制
发表时间：
2007-10-01
期刊：
影响因子：
3.4
通讯作者：
Lee, Jae K.
中科院分区：
文献类型：
--
作者：
Cho, HyungJun;Srnalley, David M.;Lee, Jae K.
LC-MS/MS与某些标记技术，如同位素编码的亲和标签（ICAT），使配对蛋白质样品的定量分析。然而，目前差异表达肽（和蛋白质）的鉴定和定量对于复杂生物样品的大蛋白质组学筛选是不可靠的。由于实验成本高和样品供应有限，重复实验的次数往往有限。传统上，使用简单的倍数变化截止值，这导致高假阳性率。由于LC-MS/MS数据的高度变异性，标准统计方法（如双样本t检验）不可靠且效力严重不足，尤其是当仅可获得少量重复样本时。使用先进的误差池技术，我们提出了一种新的统计方法，可以可靠地识别差异表达的蛋白质，同时保持高灵敏度，特别是与少量的重复。所提出的方法被施加到一个广泛的模拟研究和从血小板（血小板MP）和从血浆中分离的MP（血浆MP）产生的微粒（MP）之间的蛋白质组学比较。在这些研究中，我们显示了我们的统计分析在识别差异表达但未被其他统计方法检测到的蛋白质方面的显着改进。特别是，几个重要的蛋白质-β-珠蛋白的两个肽和血管性血友病因子（vWF）的三个肽-通过我们的方法以非常小的错误发现率（FDR）进行了鉴定，而当使用其他常规方法时，没有一个是显着的。据报道，这些蛋白质在人血细胞的微粒中具有重要作用：vWF是血小板和内皮细胞产物，与P-选择素、GP 1b和GP IIb/IIIa结合，β-珠蛋白是血红蛋白中参与红细胞运输氧气的肽之一。
LC-MS/MS with certain labeling techniques such as isotope-coded affinity tag (ICAT) enables quantitative analysis of paired protein samples. However, current identification and quantification of differentially expressed peptides (and proteins) are not reliable for large proteomics screening of complex biological samples. The number of replicates is often limited because of the high cost of experiments and the limited supply of samples. Traditionally, a simple fold change cutoff is used, which results in a high rate of false positives. Standard statistical methods such as the two-sample t-test are unreliable and severely underpowered due to high variability in LC-M S/M S data, especially when only a small number of replicates are available. Using an advanced error pooling technique, we propose a novel statistical method that can reliably identify differentially expressed proteins while maintaining a high sensitivity, particularly with a small number of replicates. The proposed method was applied both to an extensive simulation study and a proteornics comparison between microparticles (MPs) generated from platelet (platelet MPs) and MPs isolated from plasma (plasma MPs). In these studies, we show a significant improvement of our statistical analysis in the identification of proteins that are differentially expressed but not detected by other statistical methods. In particular, several important proteins - two peptides for beta-globin and three peptides for von Willebrand Factor (vWF) - were identified with very small false discovery rates (FDRs) by our method, while none was significant when other conventional methods were used. These proteins have been reported with their important roles in microparticles in human blood cells: vWF is a platelet and endothelial cell product that binds to P-selectin, GP1b, and GP IIb/IIIa, and beta-globin is one of the peptides of hemoglobin involved in the transportation of oxygen by red blood cells.