Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
Proteomics. 2012 Apr;12(8):1151-9. doi: 10.1002/pmic.201100386.
Retention time prediction of peptides in liquid chromatography has proven to be a valuable tool for mass spectrometry-based proteomics, especially in designing more efficient procedures for state-of-the-art targeted workflows. Additionally, accurate retention time predictions can also be used to increase confidence in identifications in shotgun experiments. Despite these obvious benefits, the use of such methods has so far not been extended to (posttranslationally) modified peptides due to the absence of efficient predictors for such peptides. We here therefore describe a new retention time predictor for modified peptides, built on the foundations of our existing Elude algorithm. We evaluated our software by applying it on five types of commonly encountered modifications. Our results show that Elude now yields equally good prediction performances for modified and unmodified peptides, with correlation coefficients between predicted and observed retention times ranging from 0.93 to 0.98 for all the investigated datasets. Furthermore, we show that our predictor handles peptides carrying multiple modifications as well. This latest version of Elude is fully portable to new chromatographic conditions and can readily be applied to other types of posttranslational modifications. Elude is available under the permissive Apache2 open source License at http://per-colator.com or can be run via a web-interface at http://elude.sbc.su.se.
在基于质谱的蛋白质组学中，预测液相色谱中肽的保留时间已被证明是一种非常有用的工具，特别是在设计更高效的最新靶向工作流程程序时。此外，准确的保留时间预测还可以用于提高 shotgun 实验鉴定的可信度。尽管有这些明显的好处，但由于缺乏针对此类肽的有效预测器，此类方法迄今为止尚未扩展到（翻译后）修饰肽。因此，我们在这里描述了一种新的修饰肽保留时间预测器，该预测器建立在我们现有的 Elude 算法的基础上。我们通过将其应用于五种常见的修饰类型来评估我们的软件。我们的结果表明，Elude 现在对修饰和未修饰的肽都能产生同样好的预测性能，所有研究数据集的预测和观察到的保留时间之间的相关系数范围从 0.93 到 0.98。此外，我们还表明，我们的预测器可以处理携带多个修饰的肽。Elude 的最新版本完全可移植到新的色谱条件下，并可轻松应用于其他类型的翻译后修饰。Elude 可在 http://per-colator.com 下的宽松 Apache2 开源许可证下使用，也可以通过 http://elude.sbc.su.se 的网络界面运行。
