Engineering topics
Nguyen, Thomas
Publications and source records attributed to Nguyen, Thomas.
Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses
XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the platform was developed for two-group comparisons to match the independent, “control” versus “disease” experimental design. Here, we introduce an enhanced XCMS Online interface that enables users to perform dependent (paired) two-group comparisons, meta-analysis, and multigroup comparisons, with comprehensive statistical output and interactive visualization tools. Newly incorporated statistical tests cover a wide array of univariate analyses. Multigroup comparison allows for the identification of differentially expressed metabolite features across multiple classes of data while higher order meta-analysis facilitates the identification of shared metabolic patterns across multiple two-group comparisons. Given the complexity of these data sets, we have developed an interactive platform where users can monitor the statistical output of univariate (cloud plots) and multivariate (PCA plots) data analysis in real time by adjusting the threshold and range of various parameters. On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity. The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots. The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria. The utility of XCMS functionalities is demonstrated through the metabolomic analysis of bacterial stress response and the comparison of lymphoblastic leukemia cell lines.
Metabolomic data streaming for biology-dependent data acquisition
During the last 10 years, metabolomics has emerged as a powerful technology to interrogate cellular biochemistry at the global level. Although much of the success has been driven by advances in mass spectrometry, developments in bioinformatic resources for data processing have been equally important. Additionally, the widely used metabolomic software XCMS, in particular, has undergone substantial improvements since its first introduction in 2005 (ref. 1). In addition to improved algorithms for peak picking, retention time alignment and data visualization, XCMS has transitioned from a command-line interface requiring expertise with the R programming language, to a web-based platform with a graphical user interface2. This web-based platform, which we call XCMS Online, enables thousands of users to upload their metabolomic data and perform cloud-based processing.