Untargeted Analysis of Lemna minor Metabolites: Workflow and Prioritization Strategy Comparing Highly Confident Features between Different Mass Spectrometers

Metabolomics approaches provide a vast array of analytical datasets, which require a comprehensive analytical, statistical, and biochemical workflow to reveal changes in metabolic profiles. The biological interpretation of mass spectrometric metabolomics results is still obstructed by the reliable identification of the metabolites as well as annotation and/or classification. In this work, the whole Lemna minor (common duckweed) was extracted using various solvents and analyzed utilizing polarity-extended liquid chromatography (reversed-phase liquid chromatography (RPLC)-hydrophilic interaction liquid chromatography (HILIC)) connected to two time-of-flight (TOF) mass spectrometer types, individually. This study (introduces and) discusses three relevant topics for the untargeted workflow: (1) A comparison study of metabolome samples was performed with an untargeted data handling workflow in two different labs with two different mass spectrometers using the same plant material type. (2) A statistical procedure was observed prioritizing significant detected features (dependent and independent of the mass spectrometer using the predictive methodology Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA). (3) Relevant features were transferred to a prioritization tool (the FOR-IDENT platform (FI)) and were compared with the implemented compound database PLANT-IDENT (PI). This compound database is filled with relevant compounds of the Lemnaceae, Poaceae, Brassicaceae, and Nymphaceae families according to analytical criteria such as retention time (polarity and LogD (pH 7)) and accurate mass (empirical formula). Thus, an untargeted analysis was performed using the new tool as a prioritization and identification source for a hidden-target screening strategy. Consequently, forty-two compounds (amino acids, vitamins, flavonoids) could be recognized and subsequently validated in Lemna metabolic profile using reference standards. The class of flavonoids includes free aglycons and their glycosides. Further, according to our knowledge, the validated flavonoids robinetin and norwogonin were for the first time identified in the Lemna minor extracts.

Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase

The MINERVA platform is currently the most widely used platform for visualizing and providing access to disease maps. Disease maps are systems biological maps of molecular interactions relevant in a certain disease context, where they can be used to support drug discovery. For this purpose, we extended MINERVA’s own drug and chemical search using the MINERVA plugin starter kit. We developed a plugin to provide a linkage between disease maps in MINERVA and application-specific databases of candidate therapeutics. The plugin has three main functionalities; one shows all the targets of all the compounds in the database, the second is a compound-based search to highlight targets of specific compounds, and the third can be used to find compounds that affect a certain target. As a use case, we applied the plugin to link a disease map and compound database we previously established in the context of cystic fibrosis and, herein, point out possible issues and difficulties. The plugin is publicly available on GitLab; the use-case application to cystic fibrosis, connecting disease maps and the compound database CandActCFTR, is available online.

Potensi Curcumin dan 4 Herbal Empon-Empon Dalam Memodulasi Kekebalan Sel T Terhadap Covid-19

Longer immunity to Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) infection is thought to occur through memory cellular responses by activity of specific T lymphocytes. However, most patients with Coronavirus disease-19 (Covid-19) experienced a decrease in the number of T lymphocytes or lymphopenia. Agents that help maintain T cell counts such as Curcumin appear to have played an important role during the Covid-19 pandemic. Curcumin is known to provide a balance between T cell effectiveness and T cell autoaggressiveness, as well as restoring memory T cell function as observed in tumor-induced mice. The mixture of 4 herbal extracts of empon-empon which is commonly used as herbal medicine, namely temulawak, ginger, lemongrass, and turmeric, is thought to have the same effect as curcumin. This is known from the tracing of a plant-protein-compound database which shows that there are not many compounds other than curcumin that can modulate T cells. It is necessary to study the role of Curcumin and a mixture of 4 herbal empon-empon in modulating T cells in cases of infection by the SARS-Cov-2 antigen.

Open, High-Resolution EI+ Spectral Library of Anthropogenic Compounds

To address the lack of high-resolution electron ionisation mass spectral libraries (HR-[EI+]-MS) for environmental chemicals, a retention-indexed HR-[EI+]-MS library has been constructed following analysis of authentic compounds via GC-Orbitrap MS. The library is freely provided alongside a compound database of predicted physicochemical properties. Currently, the library contains over 350 compounds from 56 compound classes and includes a range of legacy and emerging contaminants. The RECETOX Exposome HR-[EI+]-MS library expands the number of freely available resources for use in full-scan chemical exposure studies and is available at: https://doi.org/10.5281/zenodo.4471217.

Use of high resolution/accurate mass full scan/data-dependent acquisition for targeted/non-targeted screening in equine doping control

A targeted/non-targeted LC-HRMS/MS method for equine doping screening analysis was developed using a QE-Plus Orbitrap mass spectrometer combined with an in-house built compound database and spectral library.

XRD Data Visualization, Processing and Analysis with d1Dplot and d2Dplot Software Packages

The d1Dplot and d2Dplot computer programs have been developed as user-friendly tools for the inspection and processing of 1D and 2D X-ray diffraction (XRD) data, respectively. d1Dplot provides general tools for data processing and includes the ability to generate comprehensive 2D plots of multiple patterns to easily follow transformation processes. d2Dplot is a full package for 2D XRD data. Besides general processing tools, it includes specific data analysis routines for the application of the through-the-substrate methodology [Rius et al. IUCrJ 2015, 2, 452–463]. Both programs allow the creation of a user compound database for the identification of crystalline phases. The software can be downloaded from the ALBA Synchrotron Light Source website and can be used free of charge for non-commercial and academic purposes.