Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany.
Bioinformatics. 2011 Apr 1;27(7):987-93. doi: 10.1093/bioinformatics/btr051. Epub 2011 Feb 3.
Alignment of multiple liquid chromatography/mass spectrometry (LC/MS) experiments is a necessity today, which arises from the need for biological and technical repeats. Due to limits in sampling frequency and poor reproducibility of retention times, current LC systems suffer from missing observations and non-linear distortions of the retention times across runs. Existing approaches for peak correspondence estimation focus almost exclusively on solving the pairwise alignment problem, yielding straightforward but suboptimal results for multiple alignment problems.
We propose SIMA, a novel automated procedure for alignment of peak lists from multiple LC/MS runs. SIMA combines hierarchical pairwise correspondence estimation with simultaneous alignment and global retention time correction. It employs a tailored multidimensional kernel function and a procedure based on maximum likelihood estimation to find the retention time distortion function that best fits the observed data. SIMA does not require a dedicated reference spectrum, is robust with regard to outliers, needs only two intuitive parameters and naturally incorporates incomplete correspondence information. In a comparison with seven alternative methods on four different datasets, we show that SIMA yields competitive and superior performance on real-world data.
A C++ implementation of the SIMA algorithm is available from http://hci.iwr.uni-heidelberg.de/MIP/Software.
当今，由于需要进行生物学和技术重复，因此必须对多个液相色谱/质谱（LC/MS）实验进行对齐。由于采样频率的限制和保留时间的重现性差，当前的 LC 系统存在观测值缺失和保留时间在运行过程中非线性失真的问题。现有的峰对应估计方法几乎完全专注于解决两两对齐问题，对于多次对齐问题，得到的结果直接但不是最优的。
我们提出了 SIMA，这是一种用于对齐多个 LC/MS 运行的峰列表的新型自动化程序。SIMA 将层次化的成对对应估计与同时对齐和全局保留时间校正相结合。它采用了专门的多维核函数和基于最大似然估计的过程来找到最适合观察数据的保留时间失真函数。SIMA 不需要专用的参考光谱，对离群值具有鲁棒性，只需要两个直观的参数，并且自然地包含不完整的对应信息。在对四个不同数据集的七种替代方法进行比较时，我们表明 SIMA 在真实数据上具有竞争力和优越的性能。
SIMA 算法的 C++实现可从 http://hci.iwr.uni-heidelberg.de/MIP/Software 获得。
