Search Results (181)

Metabolomic aging clocks—quantitative models that estimate biological age based on small-molecule profiles in biological fluids—have become dynamic tools for assessing individual aging trajectories and predicting the risk of age-related diseases. Although NMR-based approaches have been previously reviewed, the analytical landscape of mass spectrometry (MS)-based metabolomic clocks has not been systematically assessed. This review examines the key components of the MS-based analytical workflow underlying the development of metabolomic aging clocks, including biological matrix selection, chromatographic separation strategies, MS instrumentation, data preprocessing, metabolite annotation, and machine learning-based modeling approaches. Twelve published studies on MS-based metabolomic clocks were identified and systematically compared. These clocks provide predictions of chronological age with mean absolute errors of 3.5–10 years and demonstrate robust associations between metabolomic age acceleration and cardiometabolic risk, frailty, and mortality. Recurrent age-related metabolite classes include tryptophan–kynurenine pathway metabolites, acylcarnitines, sphingolipids, modified nucleosides, and tricarboxylic acid (TCA) cycle intermediates. Currently, liquid chromatography with electrospray ionization (LC-ESI) coupled to high-resolution QTOF or Orbitrap instruments dominates current workflows, with elastic net regression being the most commonly applied modeling strategy. Significant heterogeneity in analytical conditions, incomplete methodological descriptions, and limited cross-study validation remain key obstacles to clinical application. Standardization of pre-analytical protocols, the use of certified reference materials, and harmonized validation frameworks are identified as critical priorities for advancing mass spectrometry-based metabolomic clocks toward clinical translation. Full article

Liquid chromatography–tandem mass spectrometry (LC-MS/MS) is widely employed in pesticide residue analysis. Machine learning methods for automated spectral interpretation depend on large, well-curated training datasets; however, publicly available pesticide mass spectrometry data are fragmented across heterogeneous repositories, lack standardized preprocessing, and suffer from incomplete metadata. We introduce PAID (Pesticide AI-ready Dataset), comprising two curated LC-MS/MS spectral collections derived from 15 public sources (GNPS, MassIVE, MoNA, MassBank). Starting from 91,420 raw spectra, after initial pesticide-directed screening, a seven-step reproducible pipeline—spanning multi-source integration, spectral cleaning, deduplication, metadata standardization, quality scoring, stratified splitting, and feature engineering—yields PAID-Strict (7527 spectra; 3197 compounds) and PAID-Extended (21,292 spectra; 3224 compounds). Both versions cover eight pesticide categories across QTOF and Orbitrap platforms, with core metadata fields (SMILES, InChIKey, molecular formula) exceeding 98% completeness. A feature suite of 32 chemoinformatic descriptors, 2214 molecular fingerprints, and 30 spectral features is provided alongside the spectra. Benchmark classification of the eight pesticide categories using XGBoost and LightGBM achieved 81.5% accuracy. The dataset, code, and pre-computed features are publicly available under CC BY 4.0 and MIT licenses. Full article

Organic residues were extracted from ten amphorae recovered during excavations at the Late Roman Villa del Tellaro (Noto, Sicily). The samples were analysed using liquid chromatography coupled to a high-resolution Orbitrap mass spectrometer (LC-MS). Biomarkers of plant oils, including saturated and unsaturated fatty acids (oleic, linoleic, palmitic, stearic) and the oxidation product azelaic acid, were identified in eight samples. Wine-compatible biomarkers (syringic acid, L-proline, malic acid), albeit in the absence of tartaric acid, were detected in two samples alongside the oil markers, a pattern that would be consistent with, though not in itself proof of, amphora reuse. Two further samples yielded a more saturated, degraded fatty-acid profile most parsimoniously interpreted as a strongly degraded plant oil, although a contribution of animal or fish fat (possibly garum) cannot be excluded on the fatty-acid data alone. Diterpenoid resin acids diagnostic of Pinaceae spp. pitch (dehydroabietic acid, 7-oxo-DHA, 15-hydroxy-7-oxo-DHA) were identified in all ten samples, confirming the systematic application of pine resin coatings. The assemblage comprises mainly North African types (Tripolitana II, Tripolitana III, Keay 35A/B, Keay 62Q) alongside one Eastern Mediterranean amphora (LRA8) and unidentified forms. The results offer the first archaeometric evidence for the contents of transport amphorae from the Villa del Tellaro, contributing new data on Late Antique trade between North Africa, the Eastern Mediterranean, and southeastern Sicily. Full article

In Chile, Eucalyptus globulus stands out as a significant forest species, yielding around 2 million tonnes of bark; this by-product is a valuable source of phenolic compounds. This research evaluated the valorization of E. globulus bark using alkali-assisted extraction (AAE) and obtained extracts intended to protect the wood against fungal degradation and ultraviolet (UV) radiation. The chemical and thermal properties of the extracts were characterized using total phenolic content (TPC), antioxidant capacity, FTIR spectroscopy, LC-LTQ-Orbitrap-MS, and thermal analyses (TGA and DSC). Pine wood samples were impregnated using the Bethel process, and their absorption, retention, leaching, UV resistance, gloss, and antifungal efficacy were evaluated. The AAE showed an extraction yield of 8.79%, almost double that of aqueous extraction, with a phenolic content of 970 mg GAE/100 g dry bark and good antioxidant capacity. The MS/MS analysis tentatively identified low-molecular-weight organic acids, phenolic acids, a hydrolyzable tannin derivative, ellagic acid, methylated flavonol glycosides, and an iridoid non-phenolic metabolite. Thermal analysis indicated greater stability of the alkaline extracts, with a mass loss of less than 10% up to 200 °C, and significant degradation between 220 and 300 °C. Leaching tests showed a lower release of polyphenols from alkali-treated wood, indicating reduced mobility and/or greater retention of the extractives within the wood structure. Biological assays demonstrated effective inhibition of stain fungi and strong resistance to brown rot. Furthermore, UV aging tests showed less color change (Delta E*) and greater resistance to surface degradation. These results demonstrate the potential of alkaline extracts from E. globulus bark as sustainable additives for wood protection. Full article

Background: Acute myocardial infarction (AMI) remains the most lethal critical emergency worldwide. Although Angong Niuhuang Pill (ANP) is an established rescue medicine that has demonstrated outstanding therapeutic potential for cardiovascular diseases, its modern molecular mechanism has never been systematically elucidated because of its chemical complexity and unidentified targets. Methods: This study utilizes a multi-layer analytical pipeline of AI mining, network pharmacology, transcriptomics, and experimental confirmation. The components of ANP were comprehensively identified by UHPLC-Q Exactive Orbitrap HRMS. The TranSiGen algorithm was utilized to deeply mine the data and rank the components according to their relevance to AMI. The top 20 components were selected as prior weights and introduced into network pharmacology for analysis. Subsequently, a mouse model of AMI was established by ligating the left coronary artery. Cardiac function in the mice was evaluated by echocardiography and serum biochemical indicators. The pathological changes in the heart tissue were assessed by hematoxylin-eosin (H&E) and Masson staining. Cardiac transcriptome sequencing was performed, and pathway enrichment was analyzed by KEGG. The key pathways were verified by qPCR and immunofluorescence, achieving cross-validation between AI prediction and experimental findings. Results: The identification of ANP resulted in the detection of a total of 73 compounds, and the TranSiGen algorithm was employed to prioritize these compounds, yielding a ranked list of the top 20 candidates. Functional evaluation using echocardiography, serum biochemical markers, and histopathological examination demonstrated that ANP significantly ameliorated cardiac function in mice following myocardial infarction. Integration of network pharmacology and transcriptomic enrichment identified convergent axes of IL-17 signaling and mitochondrial quality control, which were subsequently experimentally validated as mechanisms by which ANP ameliorated cardiac injury. Experimental validation confirmed that ANP downregulated protein expression of IL-17A and TNF-α, normalized PINK1 and LC3-II/LC3-I marker profiles, with concomitant p62 reduction, thereby providing comprehensive molecular evidence at both transcriptional and translational levels to support the AI-driven predictions. Conclusions: This study identified IL-17 signaling and mitochondrial quality control as pathway axes associated with ANP-mediated cardioprotection against AMI, supported by AI-driven compound screening, transcriptome-network cross-validation, and experimental confirmation. This analytical framework may be adaptable to other complex TCM formulas for mechanism exploration and clinical translation. Full article

The western honey bee (Apis mellifera) is increasingly exposed to environmental stressors that affect redox homeostasis, leading to imbalances in cellular functions. Natural bioactive compound-based nutritional strategies show promise in reducing oxidative stress while preserving redox signaling. In this study, we investigated the chemical composition, cytotoxicity, and redox-modulating effects of an aqueous extract of the edible mushroom Agaricus bisporus on the AmE-711 honey bee cell line. High-resolution Orbitrap LC–MS analysis revealed a chemically diverse extract comprising polyols, organic acids, amino acids, phosphorylated sugars, nucleotide derivatives, phenolic, and lipid-related compounds. Among the identified metabolites were mannitol, malic acid, citric acid, glutamic acid, and uridine diphosphate N-acetylglucosamine, providing a biochemical basis for potential metabolic and redox-related activity. Cell viability assays demonstrated that A. bisporus extract exhibited no significant cytotoxicity under the experimental conditions. Electron paramagnetic resonance (EPR) spectroscopy with the TEMPONE spin probe showed that untreated cells exhibited only minimal signal reduction (4.20%), while treatment with the extract alone caused a moderate decrease (12.08%), indicating the absence of reductive stress. Oxidative stress induced by hydrogen peroxide resulted in a pronounced TEMPONE signal reduction (37.88%), whereas co-treatment with the A. bisporus extract substantially attenuated this effect, lowering the signal reduction to 15.34%. These findings suggest that the aqueous A. bisporus extract may help preserve basal redox activity while attenuating peroxide-induced oxidative stress in AmE-711 honey bee cells. Rather than acting as a potent radical scavenger, the extract appears to function as a mild redox modulator or stabilizer under the tested conditions, which may be beneficial for honey bee cellular redox balance. These results support further investigation of physiologically appropriate A. bisporus-based dietary supplements for mitigating oxidative stress in apicultural systems. Full article

Cortex Dictamni, the dried root bark of the plant Dictamnus dasycarpus Turcz. from the Rutaceae family, contains alkaloids as its primary bioactive components, which exhibit a wide range of pharmacological effects. This study aims to optimize the extraction process and to characterize the chemical composition of Cortex Dictamni extract (CDE), as well as to evaluate its in vitro antioxidant and antibacterial activities. The response surface methodology (RSM) was employed to optimize the extraction process of CDE, while Q-Orbitrap high-resolution liquid chromatography–mass spectrometry (LC-MS) was utilized to identify the chemical components in the CDE. Antioxidant and antibacterial activities were evaluated using ABTS and DPPH radical scavenging assays and by determining the minimum inhibitory concentration (MIC), respectively. The results indicated that the optimized extraction yield of CDE was 44.73%. The optimal extraction conditions were: ethanol concentration of 70%, material-to-liquid ratio of 1:40 g/mL, and extraction time of 35 min. A total of 10 components were identified in the extract, including alkaloids, lactones, terpenes, and flavonoids. The extract demonstrated notable oxygen-free radical scavenging capabilities, as evidenced by its DPPH (IC50 = 0.316 mg/mL) and ABTS (IC50 = 0.166 mg/mL) values. Additionally, it exhibited antibacterial effects, particularly against Escherichia coli and Pseudomonas aeruginosa, with a minimum inhibitory concentration (MIC) of ≥128 mg/mL. CDE may serve as a potential natural compound for applications in the food and pharmaceutical industries. Full article

Background/Objectives: This study explores the roles of kynurenine and 5-hydroxytryptophan (5-HTP) in modulating gut microbiota and their potential implications for exudative age-related macular degeneration (AMD). By examining the interplay between these metabolites and the microbiome, we aim to uncover novel pathways that may influence the pathogenesis of AMD. Understanding these associations could lead to innovative therapeutic approaches for managing this leading cause of vision loss in the elderly. To investigate the roles of kynurenine and 5-HTP, alongside the composition of the nasopharyngeal microbiota, in patients with exudative AMD. Methods: Blood metabolite profiling was performed using LC–MS–based metabolomics. Metabolites were extracted with cold methanol/water containing internal standards, filtered through a 10 kDa cutoff filter, separated on a ZIC-HILIC HPLC column, and detected using an Orbitrap mass spectrometer. Metabolites were identified using MZmine 2 software. Results: Patients with exudative AMD exhibited a profound systemic shift in tryptophan metabolism, characterized by significantly lower plasma levels of 5-HTP and higher levels of kynurenine compared to control subjects (p < 0.001 for both). Logistic regression analysis confirmed that both metabolites were independent predictors of AMD status; higher kynurenine levels were associated with increased disease probability, while higher 5-HTP levels demonstrated a protective effect. The kynurenine/5-HTP ratio emerged as a robust biomarker, achieving an area under the curve (AUC) of 0.85 with an optimal threshold of 3.43 (74.1% sensitivity, 84.4% specificity). When integrated with age and gender, the diagnostic performance of the model reached an excellent AUC of 0.92. After adjusting for demographic factors, the kynurenine/5-HTP ratio remained a potent independent risk factor, with each unit increase associated with a 6.30-fold increase in the odds of exudative AMD. Conclusions: Exudative AMD is characterized by a shift in tryptophan metabolism toward the kynurenine pathway, with decreased 5-HTP, increased kynurenine, and an elevated kynurenine/5-HTP ratio. This ratio showed a strong independent association with AMD and excellent diagnostic performance, highlighting its potential as a biomarker and its role in disease pathogenesis. Full article

Conventional and emerging extraction methods for recovering phenolic compounds (PCs) from Pinus radiata bark were investigated for their potential use in bio-composites and bio-based biomaterial applications. To optimize the recovery process, a Response Surface Methodology (RSM) based on a Box–Behnken design was used to evaluate the effects of extraction time (20–100 min), temperature (20–80 °C), and water or ethanol-water solvent concentrations with β-cyclodextrin (βCD) or NaOH (0.5–1.5% w/v CD/db). Polyphenolic profiles of the extracts were characterized using Fourier transform infrared spectroscopy (FTIR), LC-LTQ-Orbitrap-MS, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were used to evaluate the thermal stability and degradation behavior of the powdered extracts. Antioxidant capacity (DPPH, FRAP, ABTS) and antibacterial activity against Escherichia coli and Staphylococcus aureus were assessed by spectrophotometric assays and the agar diffusion method, respectively. Highest extraction yields were obtained using alkaline extraction (14.32%) and ultrasound-assisted extraction (UAE) (13.86%), followed by ethanol extraction (12.74%). Minimum inhibitory concentration (MIC) for P-βCD was 0.04 mg/mL, and the minimum bactericidal concentration (MBC) was 0.32 mg/mL against S. aureus. These results suggest a strong inhibitory capacity at low concentrations and the potential incorporation of these extracts into bio-based antimicrobial biomaterials. Full article

Glycation is a type of post-translational protein modification that affects antigen self-recognition, cell signaling, the proteasomal degradation of proteins, protein solubility, and the mechanical properties of tissues. Some glycation products are able to cross-link proteins. Serum concentrations of the cross-linking GOLD (glyoxal lysine dimer) and MOLD (methylglyoxal lysine dimer), and the non-cross-linking MG-H1 (methylglyoxal-derived hydroimidazolone isomer 1) in patients with psoriasis (n = 63) and in healthy controls (n = 35) were examined using the LC-Orbitrap-MS/MS (liquid chromatography–Orbitrap tandem mass spectrometry) technique. The following indices were assessed in the patients: BSA (body surface area), PASI (psoriasis area and severity index), and DLQI (Dermatology Life Quality Index). Serum concentrations of GOLD, MOLD, and MG-H1 were found to be significantly lower in psoriasis patients compared with healthy individuals. The concentrations of GOLD, MOLD, and MG-H1 did not correlate with the indices of disease activity and severity. These results may reflect the complexity of metabolic dysregulation accompanying immune-mediated inflammatory diseases such as psoriasis. Full article

Propolis is a natural product of honey bees whose chemical composition is influenced by different plant species and environmental factors, resulting in diverse biological activities. A new propolis type, the greenish-brown propolis (GBPUP), was identified in the northeast of Brazil. This study aimed to evaluate the influence of seasonal variation in the chemical composition of GBPUP extracts over a 12-month period. LC–ESI–Orbitrap–FTMS and UFLC–DAD–UV–Vis revealed a chemical composition with some differences to that of Brazilian green propolis, with pinocembrin as the major compound, followed by galangin, pinostrobin, chrysin, artepillin C, and pinobanksin. The extracts exhibited high levels of total phenolic, flavonoid, and flavanone contents and moderate to high antioxidant activity. Circos plot analysis showed that specific metabolites were responsible for the high activity against S. aureus (artepillin C, kaempferol, and ferulic acid) and C. albicans (galangin, pinobanksin, chrysin, and pinocembrin) and for moderate antibacterial activity against E. faecalis (rutin) and E. coli (luteolin, rutin, quercetin, and caffeic acid). ANOVA simultaneous component analysis (ASCA) showed a strong correlation between the metabolites (p-coumaric acid, artepillin C, luteolin) and leishmanicidal activity. Thus, seasonal evaluation allowed the identification of bioactive molecules, the months with greater bioactivity of the GBPUP extracts representing the first comprehensive study of the seasonality of this new and promising propolis variety. Full article

Mitochondrial dysfunction profoundly alters cellular metabolism, yet its systems-level consequences remain incompletely characterized. Here, we present a comprehensive untargeted metabolomics analysis of respiratory-deficient (ρ⁰) and competent (ρ⁺) Saccharomyces cerevisiae prototrophic cells using ultra-high-performance liquid chromatography coupled to Orbitrap Fusion™ Tribrid™ high-resolution mass spectrometry. By integrating hydrophilic interaction and reversed-phase chromatography in both ionization modes, we detected ~7000 features per chromatographic condition, of which ~12% were structurally annotated through MSⁿ fragmentation and in silico spectral matching. Principal component analysis revealed distinct metabolic signatures between ρ⁰ and ρ⁺ cells, with ~73% of total variance explained by the first two components. Volcano plot and hierarchical clustering analyses identified a marked accumulation of phosphate-containing metabolites, sphingolipids, ceramides, and fatty acid residues in ρ⁰ cells, whereas amino acids, excluding arginine, cysteine, and aromatics, were enriched in ρ⁺ cells. Notably, branched-chain amino acid depletion in ρ⁰ cells correlated with impaired growth and mitochondrial stress. Pathway enrichment analysis, supported by transcriptomic integration, prompted us to further investigate reprogramming of polyamine biosynthesis and aromatic amino acid metabolism. Calibration curves constructed from certified standards validated the accuracy of the LC–MS platform and reinforced annotation confidence. Our findings demonstrate that advanced untargeted metabolomics, coupled with MS³ fragmentation and multi-omics integration, enables high-resolution mapping of metabolic reconfiguration under mitochondrial dysfunction, offering mechanistic insights into mitochondrial retrograde signaling and adaptation. Full article

Background: Low-volume trapping columns are essential for sample enrichment, desalting, and injection profile focusing on nano-LC–MS-based proteomics. They enable higher sample loading, improve chromatographic performance, and protect the analytical column by removing salts and contaminants. Recently, monolithic trap columns with micropillar architecture have emerged as alternatives to conventionally packed traps. This study compares the performance of a packed and a micropillar monolithic trap column for the analysis of tryptic peptides. Methods: A tryptic digest of HeLa cell lysate was analyzed under identical LC–MS conditions using both trap types. Peptides were detected at 214 nm and analyzed by nano-ESI on a Q Exactive Plus Orbitrap. Data were searched against the human UniProt database (February 2023) using FragPipe v20.0, and statistical evaluation of MaxLFQ intensities was performed in Perseus using Welch’s t-test and clustering analysis. Results: Over 2500 proteins were identified with both setups. The packed trap column yielded more total peptides, particularly those with post-translational modifications and higher hydrophilicity, whereas the monolithic column favored peptides of intermediate hydrophobicity. Chromatographic profiles confirmed a slight reduction in the trapping efficiency of hydrophilic peptides by the monolithic trap. Conclusions: Trap column design significantly influences peptide recovery and proteome coverage. Full article

Oxidative stress is a primary driver of diabetic nephropathy (DN), highlighting the urgent need for potent natural antioxidants. This study explored the reno-protective potential and associated mechanisms of Rhinacanthus nasutus aqueous extract (AE). Phytochemical profiling via Q Exactive HF Orbitrap LC–MS/MS and serum pharmacochemistry analysis identified 38 constituents, among which 25 bioavailable constituents (e.g., caffeic acid and naringenin) might be the key bioactive ones. In the L6 myotubes in vitro assays, AE (75 μg/mL) was observed to upregulate the PI3K/AKT and GLUT4 signaling cytokines, coinciding with enhanced glucose uptake, as confirmed by Western blot with insulin as a positive control. Furthermore, in STZ-induced DN rats, AE could reduce MDA levels (0.58 vs. 1.44 nmol/mgprot) and restore T-SOD, CAT, and GSH-Px levels (170.57, 51.93, 63.68 vs. 114.93, 40.84, 50.99 mgprot). The protective effects were accompanied by the modulation of PI3K/AKT/mTOR signaling axis. These findings suggest that AE exerts dual efficacy involving glucose uptake regulation and oxidative stress inhibition. Consequently, Rhinacanthus nasutus represents a promising natural antioxidant resource with potential for the management of DN. Full article

In recent years, xylazine has emerged as a cutting agent combined with illicit drugs to extend their effects. The present study aimed to discover drug use patterns associated with xylazine-positive and -negative urine toxicology drug screens and to assess whether xylazine can be used as a marker for exposure to designer drugs/new psychoactive substances in our study population. This is a retrospective analysis of urine toxicology results from two different analytical platforms: a targeted, structurally confirmatory, high-performance liquid chromatography–tandem mass spectrometry (LC-MS/MS) assay that quantifies 136 drugs and metabolites including xylazine; and a non-targeted ThermoFisher Orbitrap Tribrid mass spectrometry system (Thermo Scientific^TM, Bremen, Germany) in combination with database searches for the identification of drugs not captured by the targeted assay. All participants were patients receiving care through the Addiction Research and Treatment Services (ARTS), with documented substance misuse, undergoing routine urine drug toxicology testing at the iC42 Clinical Toxicology. Data analysis was performed using Sciex OS version 2.2.0.5738 after extraction using the targeted, structurally confirmatory and quantitative LC-MS/MS platform (SCIEX, Framingham, MA, USA). The drug patterns found in xylazine-positive and -negative urine samples were statistically significantly different (p < 0.001), indicating different consumption patterns associated with xylazine. Moreover, the overall concentrations of drugs (normalized to creatinine) were also statistically significantly different with higher concentrations in the urine samples that tested negative for xylazine. In contrast, samples that were positive for xylazine contained significantly higher concentrations of various designer drugs/new psychoactive substances as detected by the untargeted platform (p < 0.0001). The results indicated that xylazine has become increasingly common in Denver’s drug circulation and that xylazine may be used as a marker to prompt reflex testing with non-targeted high-resolution mass spectrometry assays in combination with database searches to test for the exposure to designer drugs/new psychoactive substances in our patient population. Full article