Treviño Victor, Yañez-Garza Irma-Luz, Rodriguez-López Carlos E, Urrea-López Rafael, Garza-Rodriguez Maria-Lourdes, Barrera-Saldaña Hugo-Alberto, Tamez-Peña José G, Winkler Robert, Díaz de-la-Garza Rocío-Isabel
Cátedra de Bioinformática, Departamento de Investigación e Innovación, Escuela de Medicina, Tecnológico de Monterrey, Guadalupe, Nuevo Leon, 64849, Mexico.
J Mass Spectrom. 2015 Jan;50(1):165-74. doi: 10.1002/jms.3512.
One of the initial and critical procedures for the analysis of metabolomics data using liquid chromatography and mass spectrometry is feature detection. Feature detection is the process to detect boundaries of the mass surface from raw data. It consists of detected abundances arranged in a two-dimensional (2D) matrix of mass/charge and elution time. MZmine 2 is one of the leading software environments that provide a full analysis pipeline for these data. However, the feature detection algorithms provided in MZmine 2 are based mainly on the analysis of one-dimension at a time. We propose GridMass, an efficient algorithm for 2D feature detection. The algorithm is based on landing probes across the chromatographic space that are moved to find local maxima providing accurate boundary estimations. We tested GridMass on a controlled marker experiment, on plasma samples, on plant fruits, and in a proteome sample. Compared with other algorithms, GridMass is faster and may achieve comparable or better sensitivity and specificity. As a proof of concept, GridMass has been implemented in Java under the MZmine 2 environment and is available at http://www.bioinformatica.mty.itesm.mx/GridMass and MASSyPup. It has also been submitted to the MZmine 2 developing community.
使用液相色谱和质谱分析代谢组学数据时，最初的关键步骤之一是特征检测。特征检测是从原始数据中检测质量表面边界的过程。它由排列在质荷比和洗脱时间二维（2D）矩阵中的检测丰度组成。MZmine 2是为这些数据提供完整分析流程的领先软件环境之一。然而，MZmine 2中提供的特征检测算法主要基于一次一维分析。我们提出了GridMass，一种用于二维特征检测的高效算法。该算法基于在色谱空间中着陆的探针，这些探针移动以找到提供准确边界估计的局部最大值。我们在对照标记实验、血浆样本、植物果实和蛋白质组样本上测试了GridMass。与其他算法相比，GridMass速度更快，可能实现相当或更好的灵敏度和特异性。作为概念验证，GridMass已在MZmine 2环境下用Java实现，可在http://www.bioinformatica.mty.itesm.mx/GridMass和MASSyPup上获取。它也已提交给MZmine 2开发社区。
