Prince John T, Marcotte Edward M
Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
Anal Chem. 2006 Sep 1;78(17):6140-52. doi: 10.1021/ac0605344.
Mass spectrometry proteomics typically relies upon analyzing outcomes of single analyses; however, comparing raw data across multiple experiments should enhance both peptide/protein identification and quantitation. In the absence of convincing tandem MS identifications, comparing peptide quantities between experiments (or fractions) requires the chromatographic alignment of MS signals. An extension of dynamic time warping (DTW), termed ordered bijective interpolated warping (OBI-Warp), is presented and used to align a variety of electrospray ionization liquid chromatography mass spectrometry (ESI-LC-MS) proteomics data sets. An algorithm to produce a bijective (one-to-one) function from DTW output is coupled with piecewise cubic hermite interpolation to produce a smooth warping function. Data sets were chosen to represent a broad selection of ESI-LC-MS alignment cases. High confidence, overlapping tandem mass spectra are used as standards to optimize and compare alignment parameters. We determine that Pearson's correlation coefficient as a measure of spectra similarity outperforms covariance, dot product, and Euclidean distance in its ability to produce correct alignments with optimal and suboptimal alignment parameters. We demonstrate the importance of penalizing gaps for best alignments. Using optimized parameters, we show that OBI-Warp produces alignments consistent with time standards across these data sets. The source and executables are released under MIT style license at http://obi-warp.sourceforge.net/.
质谱蛋白质组学通常依赖于对单次分析结果进行分析；然而，比较多个实验的原始数据应能增强肽段/蛋白质的鉴定和定量。在缺乏令人信服的串联质谱鉴定结果的情况下，比较不同实验（或组分）之间的肽段数量需要对质谱信号进行色谱校准。本文提出了一种动态时间规整（DTW）的扩展方法，称为有序双射插值规整（OBI-Warp），并将其用于校准各种电喷雾电离液相色谱质谱（ESI-LC-MS）蛋白质组学数据集。一种从DTW输出产生双射（一对一）函数的算法与分段三次埃尔米特插值相结合，以产生一个平滑的规整函数。所选择的数据集代表了广泛的ESI-LC-MS校准案例。高可信度、重叠的串联质谱被用作标准来优化和比较校准参数。我们确定，作为光谱相似性度量的皮尔逊相关系数在使用最优和次优校准参数产生正确校准方面优于协方差、点积和欧几里得距离。我们证明了对间隙进行惩罚以实现最佳校准的重要性。使用优化后的参数，我们表明OBI-Warp在这些数据集上产生的校准与时间标准一致。其源代码和可执行文件在http://obi-warp.sourceforge.net/ 以麻省理工学院风格许可发布。
