ChromAlign:: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces
ChromAlign:: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces
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DOI：
10.1021/ac060923y
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发表时间：
2006-12-15
影响因子：
7.4
通讯作者：
Huehmer, Andreas F. R.
中科院分区：
文献类型：
--
作者：
Sadygov, Rovshan G.;Maroto, Fernando Martin;Huehmer, Andreas F. R.
提出了一种对复杂混合物样品的LC-MS数据进行三维色谱面对齐的算法。该方法由两个步骤组成。在第一步中，我们预校准色谱轮廓：层析表面的二维投影。这是通过使用快速傅立叶变换进行相关分析来实现的。在该步骤中，确定最大化两个色谱线之间的重叠和点积的时间偏移量。在第二步中，该算法在参考层析表面和样品层析表面的全质量扫描之间生成相关矩阵元素。从第一步开始的时间偏移量指示可能相关的大量扫描的范围，然后仅为这些大量扫描计算相关矩阵。相关矩阵携带高度相关扫描的信息，但它本身并不确定扫描或时间对齐。对齐被确定为相关矩阵中最大化相关矩阵元素之和的路径。通过使用动态规划，降低了最优路径生成问题的计算复杂度。该程序生成时间对齐的曲面。使用来自第二步骤中第一步骤的时间偏移量减少了用于生成相关矩阵的计算时间，并加快了过程。该算法已在用C++语言开发的ChromAlign程序中实现。Windows XP下的NET2环境。在这项工作中，我们展示了ChromAlign在几个数据集的LC-MS表面比对中的应用：已知蛋白质的混合物，T细胞表面蛋白的消化样本，以及脑脊液消化的样本。ChromAlign精确地对齐了我们研究的LC-MS表面。在这些例子中，我们讨论了ChromAlign对齐的各个方面，例如恒定的时间轴移动和层析表面的翘曲。
We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the. NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.