ROCS: a reproducibility index and confidence score for interaction proteomics studies.
ROCS: a reproducibility index and confidence score for interaction proteomics studies.
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DOI：
10.1186/1471-2105-13-128
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发表时间：
2012-06-08
影响因子：
3
通讯作者：
Ewing RM
中科院分区：
文献类型：
--
作者：
Dazard JE;Saha S;Ewing RM
亲和纯化质谱（AP-MS）提供了一种鉴定蛋白质复合物和相互作用的有力手段。在解释AP-MS实验结果方面存在几个重要的挑战。首先，由于技术变异性和细胞中蛋白质相互作用的动态性质，AP-MS实验重复的重现性可能较低。第二，在AP-MS实验中鉴定真正的蛋白质-蛋白质相互作用由于高的假阴性和假阳性率而不准确。可以使用几种实验方法来减轻这些缺点，包括使用重复和对照实验以及相对定量来灵敏地区分真正的相互作用蛋白质与假蛋白质。为了解决蛋白质-蛋白质相互作用的可重复性和准确性问题，我们引入了一种两步法，称为ROCS，该方法利用指示猎物蛋白来选择可重复的AP-MS实验，并利用置信分数来选择特定的蛋白质-蛋白质相互作用。指示性猎物蛋白解释了蛋白质可识别性以及蛋白质再现性的测量，有效地允许去除贡献噪声并影响下游推断的离群值实验。然后将过滤后的实验组用于蛋白质-蛋白质相互作用（PPI）评分步骤。通过计算置信度分数来进行猎物蛋白质评分，置信度分数解释了诱饵实验中相对于对照实验的猎物蛋白质出现的概率，其中通过分别针对错误发现率和生物一致性的度量同时控制假阳性和假阴性来估计显著性截止参数。总之，ROCS方法依赖于参数估计和误差控制过程的自动客观标准。我们通过将其应用于之前发表的五个AP-MS实验来说明我们方法的性能，每个实验都包含充分表征的蛋白质相互作用，从而可以对ROCS进行系统的基准测试。我们表明，我们的方法可以单独使用，以准确识别特定的，生物相关的蛋白质-蛋白质相互作用，或与其他AP-MS评分方法相结合，以显着提高推断。我们的方法解决了AP-MS数据集中遇到的重要问题，使ROCS成为一个非常有前途的工具，无论是单独使用还是与其他方法结合使用。我们预计，我们的方法可能会更普遍地用于蛋白质组学研究和数据库，实验重现性问题出现。该方法是用R语言实现的，并且可以作为一个名为"ROCS"的R包获得，可以从CRAN存储库www.example.com免费获得。
Affinity-Purification Mass-Spectrometry (AP-MS) provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments. First, the reproducibility of AP-MS experimental replicates can be low, due both to technical variability and the dynamic nature of protein interactions in the cell. Second, the identification of true protein-protein interactions in AP-MS experiments is subject to inaccuracy due to high false negative and false positive rates. Several experimental approaches can be used to mitigate these drawbacks, including the use of replicated and control experiments and relative quantification to sensitively distinguish true interacting proteins from false ones. To address the issues of reproducibility and accuracy of protein-protein interactions, we introduce a two-step method, called ROCS, which makes use of Indicator Prey Proteins to select reproducible AP-MS experiments, and of Confidence Scores to select specific protein-protein interactions. The Indicator Prey Proteins account for measures of protein identifiability as well as protein reproducibility, effectively allowing removal of outlier experiments that contribute noise and affect downstream inferences. The filtered set of experiments is then used in the Protein-Protein Interaction (PPI) scoring step. Prey protein scoring is done by computing a Confidence Score, which accounts for the probability of occurrence of prey proteins in the bait experiments relative to the control experiment, where the significance cutoff parameter is estimated by simultaneously controlling false positives and false negatives against metrics of false discovery rate and biological coherence respectively. In summary, the ROCS method relies on automatic objective criterions for parameter estimation and error-controlled procedures. We illustrate the performance of our method by applying it to five previously published AP-MS experiments, each containing well characterized protein interactions, allowing for systematic benchmarking of ROCS. We show that our method may be used on its own to make accurate identification of specific, biologically relevant protein-protein interactions, or in combination with other AP-MS scoring methods to significantly improve inferences. Our method addresses important issues encountered in AP-MS datasets, making ROCS a very promising tool for this purpose, either on its own or in conjunction with other methods. We anticipate that our methodology may be used more generally in proteomics studies and databases, where experimental reproducibility issues arise. The method is implemented in the R language, and is available as an R package called “ROCS”, freely available from the CRAN repository http://cran.r-project.org/.
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影响因子：
64.8
作者：
Gavin, AC;Bösche, M;Superti-Furga, G
通讯作者：
Superti-Furga, G
影响因子：
64.8
作者：
Gavin, AC;Aloy, P;Superti-Furga, G
通讯作者：
Superti-Furga, G
影响因子：
4.4
作者：
Bern, Marshall W.;Kil, Yong J.
通讯作者：
Kil, Yong J.
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
3.5
作者：
Oeljeklaus, Silke;Meyer, Helmut E.;Warscheid, Bettina
通讯作者：
Warscheid, Bettina