Optimizing XCMS parameters for GC-MS metabolomics data processing: a case study.

BACKGROUND AND AIMS: Optimizing metabolomics data processing parameters is a challenging and fundamental task to obtain reliable results. Automated tools have been developed to assist this optimization for LC-MS data. GC-MS data require substantial modifications in processing parameters, as the chromatographic profiles are more robust, with more symmetrical and Gaussian peaks. This work compared an automated XCMS parameter optimization using the Isotopologue Parameter Optimization (IPO) software with manual optimization of GC-MS metabolomics data. Additionally, the results were compared to online XCMS platform. METHODS: GC-MS data from control and test groups of intracellular metabolites from Trypanosoma cruzi trypomastigotes were used. Optimizations were performed on the quality control (QC) samples. RESULTS: The results in terms of the number of molecular features extracted, repeatability, missing values, and the search for significant metabolites showed the importance of optimizing the parameters for peak detection, alignment, and grouping, especially those related to peak width (fwhm, bw) and noise ratio (snthresh). CONCLUSION: This is the first time that a systematic optimization using IPO has been performed on GC-MS data. The results demonstrate that there is no universal approach for optimization but automated tools are valuable at this stage of the metabolomics workflow. The online XCMS proves to be an interesting processing tool, helping, above all, in the choice of parameters as a starting point for adjustments and optimizations. Although the tools are easy to use, there is still a need for technical knowledge about the analytical methods and instruments used.

Coumarins from Rutaceae: Chemical diversity and biological activities.

Rutaceae is a family expressed by approximately 2100 species distributed in 154 genera widespread in tropical and temperate regions of Australasia, America, and South Africa. Substantial species of this family are employed as folk medicines. The literature describes the Rutaceae family as a great source of natural and bioactive compounds like terpenoids, flavonoids, and, especially, coumarins. To data, 655 coumarins were isolated and identified from Rutaceae in the past twelve years and, most of them, showed different biological and pharmacological activities. There are studies with coumarins from Rutaceae indicating that these compounds showed activity against cancer, inflammation, infectious diseases, and in the treatment of endocrinal and gastrointestinal conditions. Although coumarins are considered versatile bioactive molecules, until the present, there is no compiled information about coumarins from the Rutaceae family demonstrating the potency of these compounds in all dimensions and chemical similarities among the genera. The present review covers the relevant studies dealing with isolation of Rutaceae coumarins from 2010 until 2022 and outlines the current data on pharmacological activities these coumpounds. Additionally, the chemical disposition and similarity among Rutaceae genera are also statistically discussed employing PCA and HCA methods.