Plant metabolomics, lipidomics, ionomics, fluxomics, and peptidomics are essential approaches for exploring how plants respond to epigenetic, pathological, and environmental stimuli through comprehensive chemical profiling. Over the past decades, significant progress has been made in protocols and methodologies to address the challenges in sample collection and extraction. Despite these advancements, sample preparation remains intricate, with ongoing debates about the most effective strategies. This review emphasizes the importance of clear research questions and well-designed experiments to minimize complexity, save time, and enhance reproducibility. It provides an overview of the key steps in these fields, including harvesting, drying, extraction, and data pre-acquisition for major analytical platforms. By discussing best practices and common challenges, this review aims to streamline methods and promote more consistent and reliable research outcomes.

Investigation of the endophytic fungi Nigrospora sphaerica, Nigrospora oryzae, and Pseudofusicoccum stromaticum MeOH fractions isolated from the leaves of Vochysia divergens, a medicinal species from the Brazilian Pantanal, led to the identification of five compounds, namely a new compound (1E,8Z)-10,11-dihydroxy-5,5,8-trimethyl-4-oxocycloundeca-1,8-diene-1-carbaldehyde (1) and four known compounds: 5-methylmellein (2), sclerone (3), daldinone A (4), and lasiodiplodin (5). All compounds were identified using spectroscopic methods, and 1 was corroborated with mass spectrometry, while the known compounds were compared with data in the literature. The relative configuration of compound 1 was determined based on theoretical conformational studies as well as the J experimental values between the hydroxymethyne hydrogens. The antimicrobial activity of the compounds was evaluated. Promising results were obtained for compounds 2, 4, and 5 since they inhibited the bacterium Pseudomonas aeruginosa, an opportunistic pathogen, suggesting the potential of these microorganisms as a source of new antibacterial agents. Graphical Abstract

Cissus verticillata (plant-insulin) is used in the Brazilian popular medicine to treat symptoms of diabetes. Studies about its ability to contrast glycoxidative stress is lacking, which may add mechanistic information about its effects on treat diabetic complications. This study investigated the ability of Cissus verticillata leaf hydroethanolic extract (CvExt) to scavenge reactive oxygen species (ROS) and to inhibit the formation of advanced glycation end products (AGEs). ROS scavenging assays were used to test CvExt antioxidant activity. Incubations of bovine serum albumin with glucose (0.5 M) or methylglyoxal (2 mM) and CvExt (250, 125, and 62.5 μg/mL) were used to test the antiglycation activity, by monitoring fluorescent AGEs, markers of amino acid oxidation, and protein carbonyl groups (PCO). The plant extract was submitted to liquid−liquid extractions, fractions were analyzed by liquid chromatography with tandem mass spectrometry, and the data obtained were subjected to partial least-squares discriminant analysis. CvExt scavenged ROS inhibited the formation of AGEs and amino acid oxidation products, and decreased PCO levels. The main metabolites found in CvExt were flavonoids, cinnamic acid derivatives, coumarins, free amino acids, and some lipophilic compounds. CvExt inhibited glycoxidative stress in vitro, which can be associated with its complex chemical composition.

Investigating the mechanistic toxicity of plant extracts is essential for safety assessment. The predictive toxicological effects of Cedrela fissilis were evaluated, and LC–MS/MS‐based chemical profiling was performed. The hydroethanolic extract (HeECf) and ethyl acetate (EA) fraction were assessed in multimodel systems with different levels of biological organization. In Allium cepa , HeECf reduced root growth (29%–36%) and the mitotic index (50%–74%) at 500–1000 µg·mL ^{− 1} , whereas the EA fraction reduced only the mitotic index (30%–62%), with less pronounced effect. Chromosomal alterations were more frequent in HeECf than in EA. In Chinese hamster ovary cells, HeECf reduced cell viability (81%–68%) at 800–1000 µg·mL ^{− 1} and compromised membrane integrity, whereas the EA fraction showed IC ₅₀ > 800 µg·mL ^{− 1} . In Drosophila melanogaster , HeECf completely inhibited pupal development at 1000 µg·mL ^{− 1} , whereas at 600, 700, and 800 µg·mL ^{− 1} no toxic effects were observed, also partly related to xenobiotic metabolism. Thus, HeECf exhibited cytotoxic and genotoxic effects that impaired pupal development, likely driven by pentacyclic triterpenoids. In contrast, the EA fraction, enriched in flavonoids, displayed lower toxicity than HeECf. Overall, the toxicity of C. fissilis appears to be mechanistically linked to triterpenoid‐mediated cytotoxic and genotoxic damage, contributing to developmental disruption.