Discoveries

Streptomyces are soil bacteria famous for synthesizing complex natural products like antibiotics, which were traditionally thought to act as defensive shields against microbial competitors. However, a new study uncovers their predatory nature. Utilizing non-targeted mass spectrometry and SIRIUS structure annotation, researchers monitored the exact molecular events during the predation of live yeast cells by Streptomyces lavendulae. This aggressive interaction triggers a localized release of cell-wall-degrading enzymes coupled with the production of the polyene antifungal agents pentamycin and filipin III. Crucially, metabolomic profiling confirmed that the bacteria consume yeast membrane lipids (including phosphatidylcholines and phosphatidylethanolamines) as direct nutrients.

Keywords: antibiotics, bacteria, CSI:FingerID, ecology, lipids, natural products, profiling, soil

In this study, researchers investigated surface water toxicity and chemical dynamics in the Willamette River in Portland to address urban pollution from wastewater, road runoff, and industrial activities. To overcome the challenge of identifying unmonitored emerging contaminants, they utilized the SIRIUS computational platform for suspect and non-targeted chemical analyses. The findings revealed that continuous and episodic urban inputs influence present-day chemical dynamics more heavily than proximity to historical contamination. Through compound class predictions and molecular structure annotations, the team successfully linked unknown chemical features to distinct anthropogenic sources like road runoff and wastewater, while phenotypically anchored zebrafish embryo testing validated the biological hazard of the mapped chemical clusters.

Keywords: CANOPUS, CSI:FingerID, contamination, environmental protection, monitoring, toxicity, wastewater

Researchers explored how phytopathogenic Fusarium fungi isolated from papaya and pineapple adapt their chemical arsenals based on their environment. By employing co-cultivation to unlock dormant biosynthetic pathways, the team discovered extracts with potent protease-inhibitory properties and annotated 173 diverse metabolites. SIRIUS played a pivotal role in this tiered annotation strategy, enabling in silico structural elucidation and molecular formula prediction of complex polyketides, depsipeptides, and unreported derivatives that standard spectral libraries could not match.

Keywords: CANOPUS, CSI:FingerID, bioactivity, chemical diversity, drug discovery, ecology, fungi, natural products, pathogens

Researchers evaluated an automated computational workflow combining BioTransformer and SIRIUS to streamline the identification of drug metabolites. By benchmarking against six model drugs, the study demonstrated that this integration avoids exhaustive manual identification while expanding metabolome structural coverage. The approach automatically identified 62% to 100% of known drug metabolites and successfully discovered four previously unrecorded metabolites.

Keywords: biotransformation, drug discovery, drugs, metabolic pathways, pharmacology, toxicity, CANOPUS, CSI:FingerID

How do you verify the consistency of a medicine derived from four distinct natural sources? Researchers have just published a comprehensive molecular profile of Vertigoheel, an over-the-counter treatment for vertigo, using advanced metabolomics. Using SIRIUS for molecular structure annotation, the team successfully identified and traced over 24,000 molecular features from raw ingredients—like Indian berry and spotted hemlock—directly into the final tablets and drops. This study marks the first time LC-MS-based profiling has been used to confirm that neuroactive compounds such as picrotoxinin and coniine are consistently preserved across batches. It provides a robust framework for quality control and future network pharmacology studies in complex natural products.

Keywords: CSI:FingerID, natural products, pharmacology, plants, profiling

Intracellular metabolite concentrations are vital for cellular function, yet most are maintained at nearly undetectable levels. A new study answers this by profiling a metabolism-wide E. coli CRISPRi library, discovering that maintaining minimal metabolite pools is a strategic necessity for metabolic robustness. This keeps enzyme regulation precise while preventing toxic side reactions and inhibitory crosstalk. When CRISPRi knockdowns forced metabolites to accumulate, researchers used SIRIUS 6 molecular structure annotation and compound classification to successfully identify non-canonical metabolites arising from promiscuous side reactions. These minimal metabolite pools also limit flux through engineered pathways, though targeted knockdowns can intentionally raise precursor levels to boost synthetic bioproducts.

Keywords: CANOPUS, CSI:FingerID, bacteria, metabolic pathways, profiling

In a study published in The Crop Journal, researchers from the University of Copenhagen utilized SIRIUS to map the complex biochemical landscape of pea seeds. By analyzing 10 cultivars across different Danish farming sites, the team uncovered how agricultural practices and genetics fundamentally reshape seed chemistry. Using SIRIUS, they annotated 178 metabolites missing from traditional databases, classified 424 metabolites into distinct molecular families, and discovered three novel chloroauxin metabolites never before reported in pea seeds. The findings reveal that organic peas have higher levels of nitrogen-rich amino acids, and highlight significant cultivar-specific differences in antioxidants and off-flavor lipid oxidation products.

Keywords: agriculture, CANOPUS, CSI:FingerID, chemical diversity, food, halogenated compounds, metabolic pathways, plants, profiling, soil, sustainable agriculture, sustainable farming

Researchers at Wageningen University and the University of Florence investigated the prebiotic potential of ulvan, a polysaccharide derived from sea lettuce. Utilizing the SIRIUS suite for compound class prediction and molecular structure annotation, they moved beyond standard fermentation markers to identify a unique metabolic fingerprint. The team demonstrated that ulvan drives microbial metabolism by modulating tryptophan pathways to increase health-promoting metabolites and producing novel sulfur-containing markers.

Keywords: CANOPUS, CSI:FingerID, food, health, marine, metabolic pathways, microbiome

A new study investigates how red macroalgae survive under the intense UV radiation of the Peruvian coast by producing high concentrations of mycosporine-like amino acids (MAAs). The researchers used SIRIUS for compound-class prediction and molecular formula annotation, identifying 13 distinct MAAs, including rare, previously unreported analogues like palythine-serine and palythine-threonine. This discovery expands the known chemical repertoire of these algae and highlights their potential for sustainable, high-value photoprotective compounds in cosmetics and pharmaceuticals.

Keywords: CANOPUS, CSI:FingerID, cosmetics, marine, natural products, stress response

Researchers investigated unknown chemicals migrating from plastic and paper-based food packaging into our meals. Using SIRIUS, they performed non-target screening to identify 114 compounds, including hazardous plasticizers and persistent non-intentionally added substances (NIAS), and classified several as highly toxic.

Keywords: food, contamination, extractables and leachables, polymers, toxicity, CANOPUS

Researchers decoded the entry steps of diterpenoid alkaloid biosynthesis using a workflow that included SIRIUS within their untargeted LC-MS/MS pipeline to annotate molecular formulas and predict compound classes. Their findings reveal that ethanolamine serves as the primary nitrogen donor and map out six key enzymatic steps required for the de novo production of the foundational diterpenoid alkaloid atisinium.

Keywords: plants, natural products, metabolic pathways, CANOPUS

A new study published by a research team at INRAE in the Journal of Dairy Science has identified milk-based biomarkers for resilience and functional longevity in dairy goats. By subjecting goats to a nutritional challenge, researchers revealed metabolic "tells" that remain hidden under normal conditions. Using SIRIUS molecular structure annotation, the team structurally elucidated metabolites from complex MS/MS data. The study identified milk-based C4-DC carnitine and branched-chain amino acids (Leucine, Isoleucine, Valine) as key biomarkers reflecting mitochondrial efficiency during nutritional stress.

Keywords: CSI:FingerID, agriculture, animals, biomarker, food, stress response

A new study reveals that polylactic acid (PLA) bioplastics interact synergistically with nitrogen runoff to compromise coastal blue carbon ecosystems. When PLA microplastics and nitrogen fertilisers co-occur in seagrass soils, they supercharge the microbial mineralisation of organic matter, skyrocketing sediment CO2 emissions by up to 195%. To unravel the complex molecular mechanisms driving this carbon loss, researchers leveraged non-targeted metabolomics and the advanced tool SIRIUS for automated formula annotation and high-level chemical classification. They mapped significant shifts in metabolite profiles—identifying an accumulation of organooxygen compounds, hydrophobic sugar units, and carboxylic acids that signal accelerated seagrass polysaccharide decomposition driven by bioplastic hydrolysis. While conventional plastics like PET showed marginal effects, biodegradable PLA bioplastics actively fuel microbial carbon loss when combined with nitrogen runoff.

Keywords: climate change, ecology, marine, polymers, soil, environmental protection, CANOPUS

What is really in our drinking water? While regulated chemicals are routinely monitored, thousands of unregulated emerging contaminants often slip through the cracks. In a recent study published in Environmental Pollution, researchers from the University of Córdoba used SIRIUS to bridge this gap. By combining innovative supramolecular solvent extraction with LC-HRMS suspect screening, the team analyzed tap water from 12 countries. When traditional standards were unavailable, SIRIUS was critical for structure elucidation. It allowed the researchers to move beyond simple detection to high-confidence identification of complex molecules. They identified 33 Emerging Contaminants across 53 global samples, of which 25 compounds were reported for the first time in drinking water, including antioxidants, personal care agents, and industrial surfactants. The study concludes that while current health risks remain low, the ubiquitous presence of these chemicals underscores the need for broad-scope screening in routine water quality assessments.

Keywords: CSI:FingerID, contamination, drinking water, health, toxicity

A new study published in Clinical Gastroenterology and Hepatology by researchers from Aalborg University and Statens Serum Institut has identified significant metabolic alterations in patients up to 14 years before they receive a clinical diagnosis. Using untargeted metabolomics on the Danish PREDICT cohort, they found that over 1,200 metabolites--particularly lipids like eicosanoids and glycerophosphocholines--shift long before the onset of symptoms. SIRIUS compound class prediction and molecular structure annotation was critical for translating complex mass spectrometry data into biological insights. The team was able to annotate thousands of previously unknown metabolites. This provided the molecular evidence needed to link mucosal breakdown and subclinical inflammation to specific lipid profiles. 882 metabolites were significantly altered in future Crohn's Disease (CD) patients. A machine learning model based on these metabolites predicted CD with a mean AUC of 0.78. The findings suggest a prolonged pre-clinical phase where altered lipid metabolism drives or reflects early disease progression.

Keywords: health, human, diagnostics, biomarker, CSI:FingerID, CANOPUS

How do you verify the consistency of a medicine derived from four distinct natural sources? Researchers have just published a comprehensive molecular profile of Vertigoheel, an over-the-counter treatment for vertigo, using advanced metabolomics. Using SIRIUS for moleuclar structure annotation, the team successfully identified and traced over 24,000 molecular features from raw ingredients--like Indian berry and spotted hemlock--directly into the final tablets and drops. This study marks the first time LC-MS-based profiling has been used to confirm that neuroactive compounds such as picrotoxinin and coniine are consistently preserved across batches. It provides a robust framework for quality control and future network pharmacology studies in complex natural products.

Keywords: CSI:FingerID, natural products, drugs, human, health

Precision medicine requires knowing not just what drug a patient takes, but how their body processes it. Traditionally, identifying drug metabolites in human plasma required pre-existing knowledge of metabolic pathways or rare reference standards. In a new study published in Exposome, researchers from Columbia University present a breakthrough analytical framework using SIRIUS to solve this challenge. By combining LC-HRMS with molecular networking and the in silico power of SIRIUS, the team successfully annotated 127 drug metabolites and even detected unintended drug impurities in human plasma samples. SIRIUS molecular structure annotation provided high-confidence structural predictions for unknown molecular features. Benchmarking showed that the correct structure was ranked in the top 10 candidates 97% of the time. This allows researchers to monitor both parent drugs and their metabolites simultaneously, even when "unknown." This pipeline paves the way for personalized dosage and better drug efficacy by monitoring an individual's unique "metabolic phenotype" in real-time.

Keywords: CSI:FingerID, drugs, drug degradation, biotransformation, health, human

Fungi in deep-sea sediments thrive under extreme osmotic pressure, yet their adaptive strategies have long remained a mystery. A new study in Communications Biology by researchers from Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE) and Universidad Nacional Autónoma de México (UNAM) explores how black yeasts from the Gulf of Mexico reprogram their metabolism to survive. Using SIRIUS 6, researchers performed deep metabolomic profiling to identify how these "polyextremotolerants" adapt. By leveraging CANOPUS for automated chemical classification and CSI:FingerID for structural annotation, the team mapped complex shifts in fatty acids, terpenoids, and rare amino acid accumulations. Key Discoveries: Metabolic Plasticity: Salinity shifts trigger massive membrane remodeling and the production of specific oxylipins. Plant-like Response: Neophaeotheca triangularis utilizes amino acid accumulation strategies previously thought unique to plants. Novel Osmoprotectants: Identification of aminocyclitols as a new class of fungal stress-response molecules.

Keywords: fungi, marine, CANOPUS, CSI:FingerID, natural products

Air pollution is a global health threat, yet much of what we breathe remains a "dark matter" of complex chemical mixtures. A new study in Environmental Science & Technology has shed light on these hidden risks. Researchers developed a multimodal passive sampling method using silicone foam to capture everything from priority pollutants to fine particles. The integrated toxicological assays with high-resolution mass spectrometry to pinpoint which chemicals were actually driving lung cell toxicity. The team utilized SIRIUS for in-silico structural annotation of unknown features that showed high correlation with cellular oxidative stress and reduced viability. This led to the discovery of several potentially harmful substances in the air--including 2-indanone and 2-vinylpyridine--that are often overlooked in standard monitoring. This study proves that moving beyond simple "target lists" is essential, so we can finally begin to prioritize the most relevant toxic drivers in the air we breathe.

Keywords: contamination, environmental protection, toxicity, CSI:FingerID,

How do microbes adapt to "unstickable" surfaces? A new study in Scientific Reports provides multiscale insights into biofilm development on hydrophobic fouling-release coatings. By combining multi-omics with advanced chemical analysis, researchers revealed how substrate properties shape microbial survival. SIRIUS played a critical role in this discovery, providing the automated annotation and chemical classification needed to decode 1,215 features. This allowed the team to identify coating-specific signatures--like ceramides and glucosinolates--that govern biofilm resilience. Key Findings: Fungi play a significant, yet often overlooked, role in shaping biofilm architecture on low-adhesion surfaces. Substrate chemistry directly modulates the metabolome, even when taxonomic structures begin to converge. Moderate hydrodynamic stress (5 knots) reduces biomass but the core microbial community remains remarkably stable.

Keywords: marine, multiomics, CANOPUS, fungi

Reproducibility in natural product discovery is often hindered when moving from screening to large-scale production. Traditional scale-up methods focusing solely on oxygen availability often fail to replicate the complex metabolic footprints of filamentous bacteria. In a new study published in Scientific Reports, researchers from TU Dortmund University and Bielefeld University achieve a breakthrough in metabolome scalability. By employing SIRIUS for in silico structural characterization of the Streptomyces griseochromogenes metabolome, the team identified that multidimensional optimization--prioritizing cell morphology over simple bioprocess parameters--can increase metabolic overlap across systems by 50%. Key Insights: Identified the cultivation system itself as the primary driver of metabolic diversity. Annotated complex non-ribosomal peptides and siderophores using SIRIUS to track structural modifications. Demonstrated that 48 Flower Plates provide the highest metabolite diversity, outperforming traditional shake flasks.

Keywords: natural products, drug discovery, CSI:FingerID, bacteria

A new study published in Communications Biology has mapped the global signaling network of PHACTR1, a key genetic determinant of vascular disease. By integrating four 'omics layers, the team discovered that PHACTR1 controls fundamental processes including cell cycle progression, iron storage, and mitochondrial function. In complex multi-omic workflows, metabolic features often remain "unmappable" due to missing IDs. The researchers utilized SIRIUS molecular structure annotation to manually validate significantly changed features, identifying human metabolites and enabling their integration into higher-order biological pathways. This allowed the team to pinpoint specific metabolic shifts in glycine, arginine, and tryptophan catabolism driven by PHACTR1. These findings provide a systems-level roadmap for therapeutic intervention in vascular pathologies.

Keywords: CSI:FingerID, multiomics, health, human

Traditional plant decoctions are pillars of ethnomedicine, yet their highly polar nature often makes them "invisible" to standard analytical methods. In a new study published in Frontiers in Natural Products, researchers tackled this challenge by developing a comprehensive characterization workflow for Combretum micranthum (Kinkéliba). SIRIUS was instrumental in this breakthrough, providing high-confidence metabolite annotations from complex HR-MS/MS data. By integrating chemical class prediction and molecular structure identification, the team moved rapidly from raw mass spectra to the identification of 10 key metabolites. They revealed that the decoction is dominated by very polar betaine alkaloids. The analysis quantified betonicine (5.1%) and stachydrine (1.3%), compounds with known cardiovascular benefits, supporting the plant's traditional use against hypertension.

Keywords: natural products, plants, CSI:FingerID, CANOPUS

Beer production generates 85,000 tons of "trub" annually--a nutrient-rich by-product often relegated to animal feed. But what if this waste is actually a reservoir for next-generation nutraceuticals? A new study by researchers at Università degli Studi di Napoli Federico II and Università degli Studi della Basilicata utilizes a multi-step metabolomics strategy to bioprospect this waste stream. Researchers used SIRIUS for molecular structure annotation and compound classification to navigate the complex chemical space of trub extracts. The team identified 700 clustered metabolites, including 18 previously undescribed α- and β-acid analogues. Their findings reveal that trub is a rich reservoir of antioxidant compounds, specifically prenylated flavonoids and hop bitter acids, which effectively reduce intracellular oxidative stress in human cell lines. Integrating SIRIUS into their workflow allowed for the rapid dereplication of known compounds and the annotation of novel variants that expand our understanding of hop-derived chemical diversity. This workflow provides a scalable framework for the pharmaceutical and nutraceutical sectors to upcycle industrial waste into high-value ingredients.

Keywords: food, bioactivity, sustainable agriculture, CSI:FingerID, CANOPUS

Enteric methane from dairy cows is a significant contributor to greenhouse gas emissions. While certain seaweeds are known to inhibit methane, their effectiveness often depends on the concentration of specific bioactives that are hard to pinpoint in complex crude extracts. A new study by researchers from Aarhus University and University of Milan suggests the answer lies in specific lipophilic compounds. Using SIRIUS compound classification and molecular structure annotation they investigated Nordic seaweeds and linked potent anti-methanogenic activity to a specific chemical profile: prenol lipids, including diterpenoids and retinoids.

Keywords: CSI:FingerID, CANOPUS, natural products, sustainable agriculture, bioactivity

Identifying the botanical origins of yellow dyes in ancient textiles is a notorious challenge, as many plants share the same major yellow pigments, such as quercetin. Thus traditional analysis often fails to pinpoint the exact species used by ancestral artisans. A new study published by researchers at Aix-Marseille University and Avignon Université presents an LC-MS-based metabolomics workflow to analyse 14 common yellow dye plants. The team moved beyond simple pigment detection to identify highly specific "Gold" markers, which offer higher taxonomic resolution than common flavonoids. When experimental spectra yielded no library matches, SIRIUS enabled the putative annotation of unknown chemical markers.

Keywords: archeology, biomarker, natural products, plants, CSI:FingerID

Measuring metabolic health in children often requires invasive blood tests, which can be challenging for both young participants and researchers. A recent study by researchers from University of Vienna demonstrates a breakthrough in non-invasive monitoring. Using eccrine sweat collected simply from fingertips, researchers monitored the "metabolic fingerprints" of children participating in the EDDY nutritional education program. The study discovered that children with overweight had significantly higher levels of the artificial sweetener cyclamate at the start of the program. Following two years of nutritional education, these levels "normalized," mirroring the profiles of their normal-weight peers. This "sweat metabotyping" approach provides a window into dietary habits and gut microbiome health without a single needle. SIRIUS played a critical role in this discovery, providing the computational power to identify and annotate 284 high-confidence metabolites--including these key sweeteners--from complex mass spectrometry data.

Keywords: pediatric, food, health, human, monitoring, biomarker, CSI:FingerID

While land plants are a well-known source of medicinal phenolic compounds, the specialized metabolism of ferns remains largely under-investigated. Researchers at the Marburg University recently tackled this gap, conducting a comprehensive phytochemical survey of 32 species within the Blechnaceae family. The study reveals that while common antioxidants like caffeoyl-5-O-quinic acid are ubiquitous across the family, others, like rosmarinic acid, are rare and linked to specific evolutionary lineages. Most notably, the team discovered blechnic acid B, a previously unknown compound in ferns. Structural elucidation of unknown metabolites is often a bottleneck in natural product research. By utilizing SIRIUS6 molecular structure annotation, the researchers were able to rapidly turn tandem mass spectra into actionable structure information. This in-silico modeling was instrumental in identifying the blechnic acid moiety within the unknown compound, providing the essential foundation for subsequent NMR confirmation. This research demonstrates the power of combining advanced computational tools with traditional phytochemistry to map the complex "tree of life" of plant metabolites.

Keywords: plants, CSI:FingerID, natural products

Large-scale microbiome studies often struggle with a common enemy: the clock. Traditional sample processing is labor-intensive, prone to human error, and risks well-to-well contamination. Researchers need a way to process thousands of samples without sacrificing data integrity. A new study validates the "Matrix Method"--a streamlined approach using automated, barcoded tubes to extract both DNA and metabolites simultaneously. This method cuts processing time in half while significantly reducing cross-contamination risks. To ensure the metabolic signatures remained consistent, the team utilized SIRIUS6 for compound annotation across diverse samples, from human saliva to office keyboards. They determined molecular formulas and chemical classes for over 1,000 metabolites, identifying how storage buffers like isopropanol and ethanol impact the recovery of specific chemical subclasses.

Keywords: CANOPUS, human, microbiome, multiomics

Monitoring pregnancy in giant pandas is notoriously difficult due to delayed implantation and "pseudopregnancy"--where non-pregnant females show nearly identical hormonal patterns to pregnant ones. Currently, reliable diagnosis is only possible in the final weeks of gestation. A new study by a multinational research team has identified 696 discriminative features that differentiate these states by integrating polar metabolomics and steroidomics. Remarkably, metabolic changes were detected as early as the start of embryonic diapause, months before current methods can provide answers. To navigate this complex molecular landscape, the team utilized SIRIUS for isotope and fragmentation pattern analysis, enabling the putative identification of novel biomarkers--such as o-methoxyhippuric acid and n-aminodecanoic acid--where commercial standards were unavailable. These insights provide a new methodological starting point for conservationists to support breeding success in this endangered species.

Keywords: monitoring, biomarker, animals, CSI:FingerID

How do we find new medicines in 2026? Sometimes, we have to go where the sun doesn't shine. Researchers from the USP - Universidade de São Paulo and the Instituto Tecnológico da Vale Desenvolvimento Sustentável have completed a pioneering survey of the microbial "dark matter" hidden in the iron-rich caves of the National Forest of Caraj¡s. Using untargeted LC-MS/MS and SIRIUS6, the team identified 674 distinct chemical features and mapped the chemical class diversity. The isolated strains produced powerful cyclopeptides and indole alkaloids. The extracts from cave-dwelling bacteria showed nearly 100% growth inhibition against melanoma and colorectal cancer cell lines. This research highlights how advanced computational tools can turn "extreme" microbiology into a goldmine for future drug discovery.

Keywords: drug discovery, cancer, natural products, biodiversity, bacteria

A new study from researchers at Northeastern University reveals that the "aging" of rubber is far more chemically complex than previously thought. By exposing tire wear particles and turf crumb rubber to 12 weeks of natural and artificial weathering, researchers found that water and UV light significantly accelerate the release and transformation of additives. Using a combination of LC-MS/MS and SIRIUS for in silico structural identification, the team prioritized 572 potential transformation products. They found that contact with water leads to faster chemical transformation rates than dry conditions. While much focus so far was on 6PPD-quinone, this study identified 180 features related to the antioxidant TMQ, including novel oligomers. Two bioavailable compounds previously thought to be PPD-derivatives have been re-identified as TMQ oligomers. Structural elucidation through SIRIUS was essential in navigating this "dark matter" of environmental chemistry, allowing the team to annotate 45 transformation products never before reported.

Keywords: biotransformation, CSI:FingerID, contamination, environmental protection

Iron-rich minerals like hematite cover the Martian surface, but their stability makes iron difficult for life to access. Researchers are now uncovering how extremophilic life-forms might overcome this barrier, leaving "chemical fingerprints" behind for future rovers to find. In a recent study, a multidisciplinary team investigated the black fungus Rhinocladiella similis. Their findings reveal a sophisticated biological "mining" operation: the fungus uses organic acids and specialized molecules to dissolve and reduce hematite, mobilizing iron for its growth. To map these complex biological signatures, the team employed SIRIUS to predict molecular formulas and chemical classes for unknown metabolites. They annotated 47 major metabolites, including rare siderophores and redox-active polyketides. 🚀 These stable organic compounds are now considered priority targets for life-detection instruments on upcoming missions like ExoMars.

Keywords: space, astrobiology, canopus, fungi

As Arctic glaciers melt at an accelerated rate, they release vast amounts of "foreign" organic matter into our oceans. But what exactly is in this water, and how does it change as it moves from ice to sea? In a new study, researchers from Aarhus University investigated the molecular signatures of dissolved organic matter (DOM) in NE Greenland. Using non-targeted UHPLC-qTOF-MS, the team analyzed the transition from glacial rivers to the Young Sound fjord. Glacial Imprint: Both glacial and proglacial rivers carry a heavy "aliphatic" signature--simple molecules that microbes can easily consume. Catchment Contrast: The proglacial Zackenberg River delivers more complex, aromatic material (likely from thawing permafrost) compared to direct glacial melt. Rapid Processing: Once in the fjord, these riverine inputs are rapidly diluted or processed, leaving a surprisingly uniform molecular signature across the coastal shelf. The complexity of environmental DOM makes traditional identification nearly impossible. The researchers utilized SIRIUS to predict compound classes directly from MS/MS fragmentation data. This allowed them to move beyond simple elemental ratios and identify specific shifts in lipids, benzenoids, and organic nitrogen compounds, providing a much clearer picture of the Arctic's changing carbon cycle.

Keywords: climate change, environmental protection, CANOPUS

Generating consistent data across metabolites, lipids, and proteins from a single biological sample is a major challenge in systems biology. biological variability can often mask real insights when samples are processed separately. A new study by researchers at Universität des Saarlandes tackles this by optimizing multiomics protocols for HepG2 cells. By comparing monophasic bead-based extractions with traditional biphasic MTBE methods, the team identified a clear winner for streamlined laboratory workflows: a monophasic approach using 400 nm paramagnetic beads. To go beyond simple "feature counting," the researchers utilized SIRIUS for compound class prediction, allowing for a rigorous comparison of molecular coverage across different extraction techniques. This ensured that the optimized protocol wasn't just finding "more signals," but more biologically relevant organic acids and lipids. The refined monophasic workflow--coupled with a 60-minute on-bead digestion--offers a reproducible, cost-effective, and rapid solution for integrated multiomics profiling.

Keywords: multiomics, human

Marine organisms in shallow coastal waters face a constant challenge: harmful ultraviolet radiation (UVR). While it is known that fish accumulate sun-protective mycosporine-like amino acids (MAAs) from their diet, the internal distribution and diversity of these compounds have remained largely unexplored. Researchers from Universität Innsbruck Innsbruck and Universität Rostock utilized targeted and untargeted metabolomics to map these "natural sunscreens" across various organs of Baltic flatfish (flounder, plaice, and turbot). While eyes show the highest concentration of MAAs to protect vision, these compounds were also discovered in the skin and internal organs, acting as transfer points from the digestive tract. The research confirms a direct correlation between MAA levels and the Sun Protection Factor (SPF) of ocular tissues. Using SIRIUS 6, the researchers identified three previously unknown chemical structures. These potential new MAAs are likely hydroxylated derivatives of known compounds, marking the eyes as hotspots for metabolite diversity. By leveraging advanced structure elucidation and automated annotation, this research sheds light on how higher trophic level consumers adapt to solar stress through selective nutrient transport.

Keywords: CSI:FingerID, marine, animals

Every year, the coffee industry generates over 10 million tons of waste, much of which is improperly disposed of, leading to significant environmental impacts. However, these by-products--defective green beans and spent coffee grounds--are hidden reservoirs of bioactive compounds with vast potential for the nutraceutical and cosmetic industries. A recent study has provided a comprehensive chemical map of these wastes. By employing multisolvent extraction and high-resolution mass spectrometry, researchers decoded how solvent polarity and material type dictate the recovery of functional metabolites. Ethanol was most effective for recovering hydrophilic antioxidants, such as chlorogenic acids, primarily from green coffee beans. Solvents like hexane and toluene successfully targeted lipophilic fractions in spent coffee grounds, yielding dense clusters of sterols and fatty acids. The study utilized machine learning to achieve 100% accuracy in classifying waste types based on their chemical fingerprints. SIRIUS was instrumental in the systematic annotation and classification of complex metabolites, providing a clear class-level overview of the coffee metabolome. This structural insight allows for the strategic selection of raw materials and extraction methods to transform coffee waste into high-value functional products.

Keywords: CANOPUS, bioactivity, environmental protection

Understanding how Mycobacterium tuberculosis survives within the human host is critical for developing new treatments against one of the world's deadliest infectious agents. A recent study has provided new biochemical insights into how Mycobacterium tuberculosis and its close relative Mycobacterium marinum survive oxidative stress within host organisms. Researchers have known that the gene melH plays a vital role in helping Mycobacterium resist oxidative stress and persist during infection. However, the specific physiological substrates of the MelH enzyme remained unknown. Identifying these substrates is essential to understanding how the bacteria neutralize toxic threats. By employing an untargeted lipidomics approach, researchers from Stony Brook University identified the physiological substrates of the MelH enzyme. Using a combination of liquid chromatography–mass spectrometry (LC-MS) and enzymatic assays, the research team discovered that MelH functions as an epoxide hydrolase. It targets epoxy mycolic acids--complex, very long-chain fatty acids (C60–C100)--and converts them into less reactive diols. This conversion allows the bacteria to detoxify lipid peroxides generated by host defense mechanisms, ensuring their survival. SIRIUS played a key role in the annotation of these complex lipids. Dealing with high molecular weight compounds like mycolic acids presents significant identification challenges. The researchers utilized SIRIUS to predict high-precision molecular formulas and generate fragmentation trees to understand the structural composition of the lipids. This computational analysis confirmed that the substrates possessed 1–7 degrees of unsaturation and multiple oxygen atoms, matching the profile of modified mycolic acids. By pinpointing epoxy mycolic acids as the substrate for MelH, this study not only clarifies a key survival mechanism of M. tuberculosis but also highlights MelH as a potential target for new antitubercular drugs.

Keywords: drug discovery, bacteria

How many persistent chemicals are we discharging into the sea without knowing it? A new study introduces Persistence-Directed Testing, a novel approach to assessing complex industrial mixtures. By combining 60-day biodegradation tests with LC-HRMS and advanced computational tools, researchers investigated produced water from North Sea oil platforms. The results are a wake-up call for environmental monitoring: While only 4% of chemicals detected via GC-MS were persistent, a staggering 32–44% of polar chemicals detected via LC-HRMS remained after 60 days. Most of these persistent substances were previously unidentified petroleum-related compounds. The team utilized SIRIUS for systematic class prediction and structural elucidation of the persistent features. They identified N-substituted aromatic ring structures as a major persistent concern. This workflow allowed for molecular-level insights into 145 persistent features, categorized by their molecular formulas and chemical classes.

Keywords: environmental protection, marine, wastewater, CANOPUS

Understanding how Mycobacterium tuberculosis survives within the human host is critical for developing new treatments against one of the world's deadliest infectious agents. A recent study has provided new biochemical insights into how Mycobacterium tuberculosis and its close relative Mycobacterium marinum survive oxidative stress within host organisms. Researchers have known that the gene melH plays a vital role in helping Mycobacterium resist oxidative stress and persist during infection. However, the specific physiological substrates of the MelH enzyme remained unknown. Identifying these substrates is essential to understanding how the bacteria neutralize toxic threats. By employing an untargeted lipidomics approach, researchers from Stony Brook University identified the physiological substrates of the MelH enzyme. Using a combination of liquid chromatography–mass spectrometry (LC-MS) and enzymatic assays, the research team discovered that MelH functions as an epoxide hydrolase. It targets epoxy mycolic acids--complex, very long-chain fatty acids (C60–C100)--and converts them into less reactive diols. This conversion allows the bacteria to detoxify lipid peroxides generated by host defense mechanisms, ensuring their survival. SIRIUS played a key role in the annotation of these complex lipids. Dealing with high molecular weight compounds like mycolic acids presents significant identification challenges. The researchers utilized SIRIUS to predict high-precision molecular formulas and generate fragmentation trees to understand the structural composition of the lipids. This computational analysis confirmed that the substrates possessed 1–7 degrees of unsaturation and multiple oxygen atoms, matching the profile of modified mycolic acids. By pinpointing epoxy mycolic acids as the substrate for MelH, this study not only clarifies a key survival mechanism of M. tuberculosis but also highlights MelH as a potential target for new antitubercular drugs.

Keywords: bacteria, drug discovery, health

Harmful algal blooms pose significant economic and health risks to freshwater systems worldwide. A new study by researchers at University of Michigan offers critical insights into the molecular factors driving the toxicity and succession of these blooms by investigating the exometabolome (compounds released into the environment) of the cyanobacterium Microcystis aeruginosa. Out of 274 detected metabolic features, standard spectral library matching identified only 11 compounds. To characterise the remaining "chemical dark matter," the researchers employed SIRIUS to annotate molecular formulas and structures and predict chemical classes for the unannotated features. This enabled the annotation of 248 metabolites at the superclass level and 165 at the subclass level. This allowed for a comprehensive analysis of the chemical diversity that would have been impossible with library matching alone. By analysing the predicted chemical taxonomy, the study determined that nitrogen substrate availability is the primary driver of exometabolome composition, exerting a stronger influence than strain identity or the presence of toxin-producing genes. Key findings: Cultures grown on nitrate produced the most chemically diverse exometabolomes, with 55 highly abundant compounds across 20 distinct subclasses. The study identified a trade-off between fitness strategies. Nitrate enrichment promoted the release of cyanotoxins (microcystins), while reduced nitrogen forms (ammonium and urea) promoted the release of microbial sunscreens (shinorine and porphyra-334) to manage oxidative stress. Organic acids and derivatives--specifically amino acids and peptides--were the dominant compound class driving the differences between nitrogen treatments.

Keywords: CANOPUS, environmental protection, bacteria, marine

How does increased plant growth in the Arctic affect long-term carbon storage? To address this critical question, a research team utilized stable isotope-assisted metabolomics (SIAM) to reveal the complex molecular dynamics of palsa peat decomposition. The researchers investigated the "priming effect"--the potential for fresh plant litter to accelerate the decomposition of ancient, stored soil organic matter. To achieve a mechanistic understanding of these carbon transformations, the researchers required comprehensive annotation of the complex peat metabolome, extending beyond the limits of standard spectral libraries. In complex environmental samples, many significant features remain unidentified by conventional library searches. In this study, SIRIUS was deployed for systematic class prediction for metabolites that lacked high-confidence spectral library matches. This approach enabled the characterization of specific metabolite classes, including distinct nitrogen-containing compounds and polyphenols, which would otherwise have remained unannotated. Utilizing a combination of isotopic tracing and expanded metabolomic coverage, the study concluded that priming effects within active layer palsa peat are transient and minimal,. The research demonstrated that while adding litter provoked a short-term rise in CO2, this emission stemmed principally from the transformation of the fresh litter itself, leaving the pre-existing peat largely undisturbed. Furthermore, this high-resolution analysis mapped distinct metabolic pathways, such as the degradation of plant-derived flavonoids like rutin, which likely occurred via heterocyclic C-ring fission.

Keywords: climate change, CANOPUS, CSI:FingerID, plants, bacteria

How does natural hybridization shape the chemical repertoire of plants? A new study published by researchers at Max Planck Institute for Chemical Ecology and Friedrich Schiller University Jena provides deep insights into metabolic evolution, revealing that hybrid plants can achieve a "combinatorial" chemistry that exceeds the diversity of their parents. The team investigated a naturally occurring hybrid complex of Baccharis species in Chile. Using untargeted LC-qTOF-MS, they analyzed the metabolomes of the parental species and their hybrid. To understand the drivers of chemical variation, the researchers used SIRIUS for systematic metabolite annotation and class prediction for 2,049 metabolic features. This systematic classification allowed the team to sort features into 342 primary and 1,707 specialized metabolites. The hybrid species integrates the metabolic profiles of both parents, resulting in significantly higher metabolic richness and diversity. This boost in diversity is driven almost exclusively by specialized metabolites (secondary metabolism). Primary metabolism remained conserved and indistinguishable between the species.

Keywords: CANOPUS, plants, chemical diversity

Synthetic antioxidants (SAOs) are ubiquitous additives found in plastics, food, and cosmetics. Yet, understanding how humans metabolize these compounds and tracking their presence in the environment remains a significant analytical challenge. A recent study published by researchers at Eawag demonstrates how wastewater analysis can serve as a dual indicator for both human and environmental exposure to synthetic antioxidants. To achieve this, the researchers sought to identify human metabolites of synthetic antioxidants that could serve as biomarkers in wastewater, whilst simultaneously investigating the fate and removal (abatement) of these compounds throughout various stages of wastewater treatment. To identify relevant human metabolites of synthetic antioxidants in wastewater influent, the team integrated SIRIUS into their non-target screening workflow to elucidate the structures of prioritized spectral features. This led to the identification of fenozan--a metabolite formed by five different phenolic antioxidants (SPAs). The structure proposed during the screening process was subsequently confirmed using reference standards. The discovery suggests fenozan could serve as a biomarker for Wastewater-Based Epidemiology (WBE), allowing scientists to estimate population-level exposure to common antioxidants. Tools like SIRIUS are essential for translating complex spectral data into actionable chemical insights, turning a "needle in a haystack" problem into a solvable puzzle.

Keywords: epidemiology, wastewater, CSI:FingerID

While industrial hemp is widely cultivated for fiber and cannabinoids found in its aerial parts, the roots are often overlooked and treated as agricultural waste. A study published by researchers at the National Center for Agricultural Utilization Research (NCAUR), University of Illinois College of Medicine and Oak Ridge Institute for Science and Education (ORISE) demonstrates how small molecule analysis can turn this "waste" into a potential source of pharmaceutical agents. The team sought to characterize unknown peaks observed during the liquid chromatography profiling of hemp root extracts. The goal was to move beyond the well-known cannabinoids and identify other bioactive phytochemicals hidden within the complex root matrix. Using high-resolution mass spectrometry MSn data analyzed with SIRIUS, the team successfully elucidated the structures of these unknown features. Using SIRIUS's structure database search they identified specific neolignans, including dadahol A and dadahol B. The identified compounds were isolated and tested against varying cancer cell lines. The study reports that these neolignans exhibit significant cytotoxic effects on pediatric cancer cell lines.

Keywords: drug discovery, plants, CSI:FingerID

Critical insights into how Northern peatlands respond to climate warming North American peatland systems are waterlogged, acidic ecosystems that function as massive global "carbon banks" containing approximately half of Earth's soil carbon. These unique environments rely on anaerobic (oxygen-free) conditions to severely slow down the decomposition of organic matter, effectively locking away carbon for millennia. However, as these high-latitude regions experience rapid warming, scientists are racing to understand how the microbial communities hidden within these saturated soils regulate the release of greenhouse gases like CO2 and methane. A new study by researchers at Georgia Institute of Technology offers critical insights into how Northern peatlands respond to climate warming. While it is known that warming stimulates microbial communities to release greenhouse gases (CO2 and CH4), the specific metabolic mechanisms driving this in oxygen-starved peat soils have remained elusive. The researchers found that the composition of the microbial community is surprisingly resistant to warming. Instead of a shift in species, the study suggests a shift in metabolic activity. The team proposed that microbes acquire terminal electron acceptors (TEAs) by cleaving them directly from organic matter, rather than relying solely on inorganic sources. Specifically, the multi-omics data points to the cleavage of sulfate from organic sulfur compounds--such as choline-O-sulfate--as a key driver of anaerobic respiration. This mechanism helps explain the unexpectedly high CO2 production observed in these anoxic environments. Uncovering these complex metabolic networks requires precise metabolite annotation. We are pleased to see that SIRIUS was utilized in this study to enhance annotation coverage and assign compound classes to the metabolomics data. These tools were instrumental in identifying and classifying the organic substrates, such as choline-O-sulfate and nucleotides, that serve as the hidden "fuel" for these microbial processes.

Keywords: climate change, CANOPUS

A new study published by researchers from Kaohsiung Medical University and National Taiwan University demonstrates how computational mass spectrometry tools are accelerating the discovery of selective anticancer agents from unexplored natural sources. They conducted the first comprehensive chemical characterization of a coastal halophyte plant traditionally used in East Asian folk medicine. A halophyte is a plant that grows in extreme environments, specifically adapting to endure saline conditions. These plants have evolved diverse morphological, anatomical, and physiological traits to survive in such habitats, which often include arid regions. A key characteristic of halophytes is their ability to synthesize various bioactive secondary metabolites to counter environmental stressors, such as oxidative stress and high salinity. These unique, stress-induced metabolites confer resilience to the plant against its harsh environment. The researcher team successfully utilized SIRIUS for metabolite annotation and compound classification and identified "Tryptophan alkaloids" and "Triterpenoids" as the predominant superclasses. Further classification revealed a high intensity of "Tetrapyrroles and derivatives" (chlorophylls). The team used these computational classifications to prioritize specific fractions enriched in triterpenoids and tetrapyrroles for targeted purification. This computationally guided approach led to the isolation of eight previously undescribed metabolites, including new triterpenoid saponins and chlorophyll derivatives. Newly identified chlorophyll-b-type compounds exhibited potent cytotoxicity against human colorectal cancer cell lines. Crucially, these compounds demonstrated selective toxicity, showing minimal effects on normal epithelial and fibroblast cells. This study is the first report of anti-CRC activity for pyran ring-type chlorophylls, highlighting their potential as therapeutic leads. The study design underscores the importance of computational tools such as SIRIUS in prioritizing bioactive candidates and streamlining the natural product discovery pipeline.

Keywords: cancer, drug discovery, plants, CANOPUS, health

The maturation of the gut microbiome during the first six months of life is a foundational process, playing a key role in metabolic programming and training of the immune system. A new multi-omics study published by a research team around Lars Bode, Pieter C. Dorrestein, and Rob Knight (University of California, San Diego) offers unprecedented insight into how maternal and environmental factors shape the infant gut in low- and middle-income countries (LMICs) by profiling 55 mother-infant pairs in Bangladesh using a multi-omics approach. Systematic classification and metabolite annotation was achieved using SIRIUS. The overall aim was to understand how maternal and environmental factors--specifically delivery mode, maternal milk composition, and household water treatment--shape this foundational postnatal development. SIRIUS was instrumental in characterizing a key metabolite associated with maternal secretor status--a candidate trihydroxy bile acid consistently elevated in infants of secretor mothers. SIRIUS provided class predictions for thousands of features. For example, it identified that the metabolic differences driving maternal secretor status were largely attributable to saccharides, steroids, and sphingolipids. Molecular networking, supported by these annotations, confirmed that Human Milk Oligosaccharides abundant in secretor milk were enriched in the feces of the respective infants, directly linking maternal genetics to the infant chemical environment.

Keywords: microbiome, human, CANOPUS

Novel insights into the macroevolutionary patterns driving phytochemical diversity in island floras. Researchers investigated 54 endemic and native non-endemic vascular plant species across four islands in the Macaronesian Canary Archipelago to determine the roles of island residence time (proxied by mean crown node age) and climate on specialised plant chemistry. To comprehensively assess plant specialised chemistry, UHPLC/MS analyses were performed on leaf samples. SIRIUS was applied to identify metabolite structures and predict compound classes. The compositional variation across different specialized metabolite groups revealed detailed shifts associated with crown age and climate: Increasing crown age was positively associated with the expression levels of specific specialised nitrogen-based metabolites and carbon-based metabolites. Conversely, groups like amino acids and carbohydrates were underexpressed with increasing crown age. Temperature and precipitation were significant predictors of phytochemical diversity. Higher chemical diversity was associated with colder and wetter conditions. For instance, certain alkaloids were overexpressed in warmer climates (consistent with roles in thermal damage protection), while phenolics were underexpressed with increasing temperature (suggesting an adaptive role in colder environments).

Keywords: plants, chemical diversity, climate change

This untargeted breathomics study from Saarland University has uncovered a promising non-volatile endogenous biomarker candidate in human exhaled breath aerosol. The identification of such a robust marker is a significant step toward overcoming the current primary limitation in exhaled breath analysis: the lack of standardization in sample collection. Researchers applied liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS/MS) to analyze exhaled breath microparticles collected from healthy volunteers and patient samples. The core challenge was identifying endogenous, non-volatile compounds that could serve as a reliable reference for the amount of exhaled breath collected. Following extensive feature filtering, the remaining candidate features were analyzed using various spectral libraries and SIRIUS 6. Although a distinct molecular match for the most robust feature was not obtained, SIRIUS successfully classified it as a long-chain fatty acid compound. The feature's consistency and robustness across different populations--healthy volunteers and an older patient cohort with chronic conditions--strongly supports its potential as an endogenous biomarker candidate for standardizing exhaled breath sample collection.

Keywords: health, human, biomarker

A recent untargeted metabolomics study employed SIRIUS 6 to characterize the bioactive potential of Ficus racemosa fruit extracts to uncover its therapeutic potential. The comprehensive analysis investigated the influence of drying methods and solvent concentrations on the metabolite composition and crucial biological activities, particularly inhibition of enzymes critical for managing postprandial hyperglycemia. The study found that the freeze-dried (FD) sample extracted with 100% ethanol exhibited the highest biological activity that positions the F. racemosa extract as a promising natural source for managing glycemic control. The application of SIRIUS enabled the robust identification of key secondary metabolites within molecular clusters related to antidiabetic activity.

Keywords: plants, food, drug discovery, health

The "chemical pollination syndrome" is a hypothesis proposing that nectar chemistry provides evidence of convergence across functional pollinator groups, similar to how physical features converge. A recent study by researchers at University of Texas at Austin, University of California Davis and Smithsonian Tropical Research Institute utilized untargeted metabolomics and metabolite identification and classification with SIRIUS to test for this hypothesis. They provide strong evidence that floral reward chemistry evolves adaptively in response to functional pollinator groups. The study compared nectar and leaf chemistry across 19 Salvia species exhibiting bee- or hummingbird-syndromes. The core discovery is that independently derived bird-syndrome nectar showed convergence on chemical traits distinct from bee-syndrome nectar. This chemical convergence supports the hypothesis that nectar metabolomes contribute to pollination syndromes. The pattern was primarily driven by the composition and concentration of alkaloid profiles.

Keywords: plants, chemical communication, CANOPUS

Advancement in Coral Restoration Groundbreaking work in ecological engineering has successfully leveraged advanced small molecule analysis to overcome a critical bottleneck in coral reef recovery: successful larval recruitment. Researchers from University of California San Diego, University of Milan, University of Hawaii, University of Amsterdam, and Mario Negri Institute for Pharmacological Research developed SNAP-X, a hybrid biomaterial that mimics the chemical landscape of healthy reefs, resulting in an over 20-fold enhancement of coral settlement compared with control substrates. The essential foundation for this biomimetic approach was the detailed molecular characterization of the settlement-inducing exometabolites derived from crustose coralline algae (CCA). SIRIUS played a critical role in elucidating the molecular composition of this chemical mixture. The researchers identified relevant chemical classes, including carboxylic acid derivatives, carbohydrates and conjugates, amino acids, steroids, fatty amides, and ethers. These molecular insights enabled the successful engineering of SNAP-X, a nanoparticle-biopolymer delivery system designed for the sustained release of these chemical signals.

Keywords: marine, CANOPUS

Decoding a Three-Way Chemical Crosstalk in Cystic Fibrosis Lungs In the complex environment of the Cystic Fibrosis lung, infections are rarely caused by a single pathogen. Instead, they are often polymicrobial, involving a mix of bacteria and fungi that are incredibly challenging to treat. A new study from researchers at the Georgia Institute of Technology's School of Chemistry and Biochemistry and Center for Microbial Dynamics and Infection investigated the polymicrobial interactions between the bacterium Burkholderia cenocepacia and the fungus Aspergillus fumigatus. Their work focused on how the clinically administered antibiotic trimethoprim influences their interaction. SIRIUS was instrumental in identifying the chemical structures of previously unknown molecules from the MS data to annotate key compounds. The results show that antibiotics can act as more than just microbial inhibitors; they function as powerful signaling molecules that fundamentally reshape the dynamics between kingdoms. 'Trimethoprim stimulates B. cenocepacia to produce an antifungal compound called fragin, which inhibits the growth of A. fumigatus. 'A. fumigatus actively defends itself by chemically modifying and inactivating the bacterial weapon, fragin. 'The presence of both the bacteria and trimethoprim leads to significant changes in the fungus. The researchers observed the modification of ergosterol--a vital component of the fungal cell membrane and a major target for antifungal drugs. Trimethoprim also directly disrupted the fungus's ability to produce a pigment crucial for its virulence. The study underscores that the chemical landscape within the Cystic Fibrosis lung, including the presence of therapeutics, is a critical factor influencing pathogen behaviour. This deeper insight into polymicrobial interactions is essential for characterising pathogenic phenotypes and may contribute to developing more effective treatments for microbial infections.

Keywords: antibiotics, drug discovery, health, human, bacteria

Beyond the Molecule: SIRIUS Helps Uncover New Metabolic Pathways in Ruminant Nutrition Flavonoids like rutin and quercetin are widely used as powerful antioxidant supplements to improve livestock health and productivity. However, the exact metabolic pathways these compounds follow within ruminants have not been fully understood, creating uncertainty about their mechanisms of action. Researchers from Gifu University employed an untargeted metabolomics approach using molecular networking to map the biotransformation of rutin and quercetin in detail. The researchers used SIRIUS, to help identify the chemical structures of unknown metabolite candidates from tandem mass spectrometry (MS/MS) data. The study confirms that rumen microorganisms first degrade rutin to produce quercetin. Quercetin is then broken down into various smaller phenolic compounds. The study is the first to identify 3-(3-hydroxyphenyl)propanoic acid (3-HPPA) as a quercetin metabolite in ruminants. The detailed metabolic map clarifies which compounds are ultimately active in the animal's body, and which metabolites are found in the blood. Understanding these pathways is essential for formulating more effective nutritional supplements to optimise animal health and productivity. This research can inform future feeding practices and supports the use of flavonoids as a tool for more sustainable livestock management.

Keywords: animals, biotransformation, sustainable farming

Unlocking the Metabolic Secrets of Crucial Marine Plankton A new study published by researchers from Friedrich Schiller University Jena, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Sorbonne Université and Université Grenoble Alpes provides unprecedented insight into the metabolic interdependence between radiolaria--ubiquitous marine plankton--and the symbiotic microalgae they host. These organisms are among the most important primary producers in low-nutrient ocean areas and play a vital role in the global carbon cycle, but they have remained poorly understood because they cannot be cultured in a lab. The study investigated two highly abundant photosymbiotic radiolaria, Collodaria and Acantharia, comparing their metabolic composition to that of their free-living algal partners. Using advanced techniques like liquid chromatography-high resolution mass spectrometry (LC-HR-MS) and mass spectrometry imaging, researchers mapped their complex biochemical relationship. A critical part of the workflow involved using SIRIUS for the annotation of unknown metabolites, allowing for the identification of key chemical compounds.

• The study found that the metabolism of the algae changes significantly when living inside the host. The largest group of detected metabolites was unique to the symbiotic partnership (the holobiont), suggesting the host either transforms algal metabolites or that new metabolic pathways are activated during symbiosis.
• A major difference was observed in the composition of phospholipids between free-living and symbiotic algae. This indicates a rearrangement of the algal cell membrane is required to adapt to the symbiotic lifestyle.
• The algae appear to provide their hosts with protective osmolytes like DMSP (dimethylsulfoniopropionate). Mass spectrometry imaging revealed the presence of DMSP in both the symbiont and host cells, suggesting algae provide osmolytic protection to their host. The findings also suggest a possible dependence of Collodaria on its symbiont for vitamin B3.

These results demonstrate a strong, complex interdependence in radiolaria-microalgae photosymbioses. Understanding these mechanisms is essential for predicting how these vital planktonic communities will respond to environmental changes, which could have unforeseen consequences for our ocean's ecosystems on a global scale.

Keywords: marine, environmental protection

Crop Resilience: New Insights into Common Bean's Defence Against Rust Fungus Fungal pathogens like rust, caused by Uromyces appendiculatus, present a growing threat to the yield and quality of the common bean (Phaseolus vulgaris L.), a vital crop for global food security. A new study by researchers from University of South Africa provides critical insights into the molecular mechanisms that underpin the common bean's defence strategies. They used an integrated metabolomics and transcriptomics approach to compare a rust-resistant bean variety with a susceptible variety. The study successfully profiled the precise molecular changes that occur when the plant is infected. SIRIUS 6 was instrumental in processing the mass spectrometry data, enabling the chemical class prediction and structural annotation of the metabolites that were key to the plant's defence response.

• The researcher identified over 3,000 differentially expressed genes and 30 known metabolites (including flavonoids, lipids, and phenylpropanoids) that are triggered by the rust infection.
• The resistant variety showed a distinct ability to up-regulate key defence-associated metabolites. In contrast, the susceptible variety down-regulated these compounds, suggesting a weakened defence response.
• Integrative analysis revealed complex correlations between specific genes and metabolites, indicating that the timing and coordination of these molecular responses are vital for effective resistance.

These findings provide a foundational understanding of the gene-metabolite linkages in common bean resistance and can inform targeted breeding techniques to accelerate the development of rust-resistant varieties.

Keywords: plants, crop protection, sustainable agriculture, defense

Unlocking Bacterial Chemistry: How Cultivation Systems Drive Natural Product Discovery The search for novel bioactive molecules from bacteria is a cornerstone of drug discovery, but it is often hindered by the repeated rediscovery of known compounds. A new study published by researchers from TU Dortmund University offers a crucial insight into overcoming this challenge. They have conducted the first comprehensive assessment demonstrating that the choice of cultivation system has a significant impact on the bacterial "metabolic footprint" --the collection of secondary metabolites they produce. The team compared the growth and secondary metabolite formation of four bacterial species across various platforms, including traditional shake flasks, stirred tank bioreactors, and highly parallelised microtiter plate cultivation systems. They analysed the bacterial extracts using LC-MS/MS, and annotated the detected mass features with SIRIUS.

• While bacterial growth was good in most systems, the secondary metabolites produced showed considerable divergence. The maximal overlap of produced molecules between the different systems was only 31%, indicating that each method unlocks a different part of the bacteria's chemical potential.
• The impact was most pronounced for filamentous bacteria, such as Streptomyces, which are known producers of important natural products.
• This work confirms that microtiter plate cultivation systems provide a robust platform for parallelising experiments, allowing scientists to simultaneously test many conditions and access a broader chemical space in the search for novel natural products.

This study provides valuable insights for future natural product screening campaigns. It demonstrates that varying the cultivation system is a powerful strategy for influencing the production of secondary metabolites and their chemical derivatives.

Keywords: natural products, drug discovery, bacteria, health

Common Chemicals Linked to Ovarian Malignancies A new study by researchers from Jozef Stefan Institute and University of Ljubljana has uncovered potential links between exposure to common environmental chemicals and ovarian malignancies. Using a nontargeted screening method, researchers have identified key differences in the chemical profiles of women with ovarian malignancies compared to healthy individuals. The study employed a non-targeted high-resolution mass spectrometry-based approach to analyse urine samples from 25 women with ovarian malignancies and 25 healthy controls. SIRIUS was used to identify the chemical compounds detected allowing the team to propose structural candidates for unknown compounds by matching their mass spectra against chemical databases. This was essential for annotating biomarkers that were not present in existing spectral libraries. The key discovery of the study is that women with ovarian malignancies had significantly higher urinary levels of six specific biomarkers of exposure compared to healthy controls. The identified biomarkers were two phthalates, two pesticides, a UV filter, and an industrial byproduct. These compounds are known or suspected endocrine-disrupting chemicals that may interfere with hormonal regulation, potentially contributing to cancer development The study highlights a strong association and does not establish causation. It demonstrates the power of nontargeted urinary profiling in chemical exposure assessment. These findings provide valuable insights into the potential role of endocrine-disrupting chemicals in hormone-sensitive cancers and support the development of next-generation chemical risk assessments.

Keywords: cancer, health, human, contamination

Unravelling the Wasp Moth's Chemical Defence New research by scientists from Macquarie University and Max Planck Institute for Chemical Ecology on the red-necked wasp moth (Amata nigriceps) has uncovered surprising details about its chemical defences, providing new insights into the link between its conspicuous warning signals and its chemical composition. Using an untargeted metabolomics approach, researchers analysed the moth's chemical makeup with UPLC-MS. SIRIUS was used to analyse the data and identify molecular structures.

• The study ruled out the presence of pyrrolizidine alkaloids (PAs), a class of defensive compounds commonly found in other arctiine moths.
• The untargeted metabolomics approach suggests that the moths may instead sequester other compounds for defence, such as steroidal alkaloids and alkylbenzenes.
• A remarkable difference was found between sexes. The analysis identified 474 compounds, with 107 being at least ten times more abundant in females than in males. In contrast, only eight compounds were ten times more abundant in males. This suggests females have higher concentrations of these potential defensive chemicals.

Non-targeted analysis using SIRIUS can reveal novel defensive strategies in nature and deepen our understanding of the complex trade-offs associated with aposematic traits.

Keywords: chemical communication, defense, ecology, animals, entomology

Hidden Emissions: PFAS Byproducts Identified in Air Near Fluoropolymer Plant using SIRIUS A recent study in the Netherlands investigating airborne per- and polyfluoroalkyl substances (PFAS) has identified a series of previously unmonitored compounds 25 km downwind of a fluoropolymer production plant. The main objective was to investigate the processing aid HFPO-DA and suspected PFAS before and after the installation of new emission abatement systems to assess their efficacy. They found the emission abatement systems to be effective in significantly reducing emissions of the processing aid HFPO-DA. While the research primarily targeted known processing aids, the team also employed a "suspect screening" approach to search for other potential contaminants. Using SIRIUS, they detected a homologous series of suspected polymerization byproducts identified as hydrogen-substituted perfluoroalkyl carboxylic acids (H-PFCAs), including at least seven homologues. H-PFCAs are known byproducts of PTFE polymerization. The identities of three of these H-PFCAs were confirmed by acquiring authentic standards. Air concentrations of these newly identified H-PFCAs peaked in the same samples that showed high levels of the processing aid, suggesting they were released from the same source--the fluoropolymer plant. This discovery underscores the complex mixture of PFAS emitted by fluoropolymer facilities and highlights the importance of using comprehensive, non-targeted analytical methods to gain a complete picture of industrial air emissions.

Keywords: pfas, contamination, biocontrol, environmental protection

Unlocking a 50-Year-Old Fungal Secret: The Biosynthesis of 6-PP Revealed For more than half a century, the exact origin of 6-pentyl-alpha-pyrone (6-PP)--a key metabolite from Trichoderma fungi--has remained unresolved. This compound is well-known for its pronounced antifungal and plant growth-promoting properties, making it vital for biological pest control. A new study published by researchers at University of Innsbruck has finally elucidated the molecular pathway behind this important compound. SIRIUS was used for data evaluation from LC-HRMS during the specialised metabolite analysis. Key findings from the study include: - 6-PP is produced via the polyketide biosynthesis pathway, with Pks1 (polyketide synthase) being the crucial enzyme. - The deletion of the pks1 gene in T. atroviride causes a complete loss of 6-PP production. SIRIUS helped with the identification of 6-PP as well as nine putative 6-PP derivatives that were present in the wild-type strain but missing in the mutant. - The loss of pks1 resulted in a significant reduction in the fungus's ability to inhibit the growth of plant pathogens. This breakthrough provides novel insights into one of the most significant compounds produced by this mycoparasitic fungus. These findings may pave the way for developing improved biocontrol agents and using 6-PP as a potent biopesticide, supporting an eco-friendly and sustainable approach to plant disease management.

Keywords: sustainable agriculture, fungi, plants, pathogens, environmental protection

It's Not Just the Salt, It's the Anion: Willow's Sophisticated Defence Revealed A new study on the willow cultivar Salix miyabeana ‘SX64' reveals a highly sophisticated aspect of plant salt tolerance. The study demonstrates that the willow's metabolic response to soil salinity is vastly different depending on the specific salt anion (chloride vs. sulphate) present. This detailed investigation was done using untargeted metabolomics, detecting over 5,000 metabolic compounds across the willow's roots, stems, and leaves. Interpreting this vast and complex dataset required advanced computational tools. The researchers used SIRIUS to identify the chemical structures of unknown compounds from mass spectrometry data. Key findings include: -The willow cultivar maintained its biomass productivity even at high soil salinity levels, confirming its suitability for phytoremediation and use as a feedstock on salt-impacted lands. - When exposed to moderate levels of sodium chloride and sodium sulphate, only 3% of the differentially abundant metabolites showed a common, or 'generalised', response to salinity. The overwhelming majority of metabolic changes were specific to the anion. - Sodium chloride stress led to a reduction in carbohydrates and key energy cycle intermediates, suggesting pressure on the plant's carbon and energy resources. The plant responded by accumulating antioxidant flavonoids and compounds for root structuring. - Sodium sulphate stress triggered the accumulation of sulphur-containing peptides, indicating that the willow may incorporate excess sulphate into specialised metabolites to mitigate ion toxicity. - Metabolic responses were highly localised. The roots, as the frontline of exposure, exhibited the most extensive biochemical changes to protect the rest of the plant. This research underscores that characterising soil salinity by electroconductivity alone may be insufficient. The specific ionic composition of the soil is a critical factor that drives distinct metabolic responses in plants. These insights are crucial for developing more effective phytoremediation strategies and breeding crops with enhanced, tailored salt tolerance mechanisms.

Keywords: chemical communication, plants, defense, sustainable agriculture

The Lipid Signature of Survival: Uncovering a Key to Coral Heat Tolerance New research published by researchers at University of Hawai‘i at Manoa offers key insights into how coral symbionts adapt to heat stress at a molecular level, a critical area of study for understanding coral reef persistence under climate change. They exposed genotypes of the coral Montipora capitata--hosting either the thermosensitive symbiont Cladocopium or the thermotolerant symbiont Durusdinium--to an 8-day heat stress experiment. They found that - the metabolic profiles of the coral holobionts were primarily shaped by the identity of the symbiont genus (Cladocopium or Durusdinium). - under heat-induced oxidative stress, the betaine lipids in the thermosensitive symbionts were remodelled to more closely resemble the abundance and saturation state of those in the thermotolerant symbionts. - heat-induced stress modulates the symbionts' cell surface glycan composition, which is believed to play a role in host-symbiont recognition and affinity. This in-depth biochemical analysis was conducted using untargeted metabolomics and chemical classification of metabolite features was performed using SIRIUS. Through this classification, the researchers identified 11 molecular families. This step allowed them to discover that glycerophosphocholines, betaine lipids, and fatty acylcarnitines were particularly influential families in distinguishing between the two symbiont types. The remodelling of membrane lipids may be a key strategy that Symbiodiniaceae members use to cope with stress. Understanding these cellular mechanisms helps identify traits contributing to coral resilience and sheds light on the plasticity of the coral-symbiont relationship in response to rising sea temperatures.

Keywords: marine, climate change

A recent study by researchers from Seoul National University details the genetic and metabolic basis for the production of sesquiterpenoids in the medicinal mushroom Sanghuangporus, which is highly valued in East Asian medicine for its therapeutic properties. The bioactive sesquiterpenoids are linked to the mushroom's remedial effects. The study sought to predict the sesquiterpene synthase gene, its associated biosynthetic gene cluster (BGC), and the pathway for a group of abscisic acid-related sesquiterpenoids. They predicted a putative biosynthetic gene cluster that contains a conserved sesquiterpene synthase gene. SIRIUS was instrumental in effectively identifying the target cluster of sesquiterpenoids from the mushroom extracts when combined with feature-based molecular networking. It provided molecular formula and substructure annotations for the compounds within the target cluster based on their fragmentation patterns. The study discovered a new abscisic acid-related sesquiterpenoid, named SHA-1, alongside six known compounds. SIRIUS was instrumental in this process, used for MS2 fragmentation analysis to identify molecular formulas and for substructure annotation, which helped pinpoint the target compounds.

Keywords: natural products, fungi

Hidden Players in Drug Efficacy In pharmacology, one of the most significant challenges is the variability in how patients respond to the same drug. While factors like genetics and lifestyle are known to play a role, emerging research points to a hidden player: the human gut microbiota. This vast community of trillions of microbes is an active participant in our health, influencing everything from nutrient absorption to the efficacy of our medications. A recent study by researchers at Yale University and the University of Pittsburgh reveals how this vast microbial community can metabolize and alter GPCR drugs--one of the most successful classes of pharmaceuticals. Using advanced tools like SIRIUS, they identified novel metabolic pathways where bacteria can either activate or inactivate medications. Gut bacteria can perform sophisticated chemical changes, like adding sulfur to drugs, creating previously unknown metabolites. The bacterium Morganella morganii was shown to inactivate the drug iloperidone by using amino acids. The study confirmed that metabolic changes directly affect drug function, showing some drugs were activated by bacteria, while others were inactivated. This research highlights the critical role of the gut microbiome in shaping therapeutic outcomes. Understanding these interactions is a crucial step toward personalized medicine and developing more effective drug therapies.

Keywords: microbiome, drug discovery, biotransformation, drug degradation, human, health

The quest to enhance long-term soil carbon storage Root exudates are the diverse collection of small molecules that plants release from their roots into the surrounding soil. These compounds represent a significant input of carbon to the soil, estimated to be about 9% of the total organic carbon fixed by plants through photosynthesis. While root-derived carbon is known to contribute more to soil carbon stocks than aboveground litter, the precise molecular diversity of these exudates is not yet fully understood. New research from scientists at Pacific Northwest National Laboratory reveals the significant role of plant root lipids in soil carbon dynamics, offering new avenues for enhancing long-term carbon storage. They have performed the first comprehensive "metabo-lipidome" characterization of root exudates from tall wheatgrass. As standard library searching could only annotate about 3.5% of the detected metabolite features, SIRIUS compound class prediction was essential for annotating 80% of the previously unknown metabolite features, with 'Organic acids and derivatives' and 'Lipid and lipid-like molecules' being the most predominant chemical superclasses. The researchers discovered a surprising diversity of lipids -- including substantial levels of triacylglycerols, fatty acyls, sphingolipids, and sterol lipids -- some of which had never been documented in root exudates before. The lipids possess a high carbon-to-nitrogen ratio and a highly negative nominal oxidation state of carbon. This indicates they are thermodynamically less favorable for microbial decomposition, suggesting they have a greater potential to persist in the soil and contribute to long-term carbon storage. This molecular-level understanding of the soil carbon cycle provides a scientific basis for developing new agricultural strategies aimed at enhancing long-term carbon storage in soil to mitigate climate change. Ultimately, these insights could inform future strategies to breed or engineer plants with exudate chemistry optimised for enhancing soil health and carbon sequestration.

Keywords: climate change, environmental protection, lipids, soil, sustainable agriculture, plants

A study on the marine dinoflagellate Amphidinium eilatiense has identified bioactive compounds with selective cytotoxic activity against human breast and lung cancer cell lines. Using untargeted metabolomic analysis on the most cytotoxic fractions and SIRIUS for structure annotation and chemical class assignment, they found that the observed cytotoxicity was not primarily linked to the previously studied polyketide toxins. A complex profile of other compounds, including fatty acids, alkaloids, and peptides seems to be responsible for, or contribute synergistically to, the observed anticancer effects. Several compounds with previously reported anticancer properties, such as erucamide, linoleamide, and ergosterol, were putatively identified in the bioactive fractions.

Keywords: marine, cancer, human, drug discovery, natural products

A new study by researchers from University of California, Davis investigated the potential link between chemicals in drinking water and regional differences in breast cancer incidence in California. As a majority of breast cancers are estrogen-dependent, meaning their growth can be stimulated by chemicals that activate estrogen receptors, they analysed 270 water samples (sourced from 120 households and 15 different brands of retail bottled water) to find chemicals potentially linked to estrogenic activity. Using liquid chromatography with high-resolution mass spectrometry, researchers detected over 7,500 molecular features, prioritising a subset of 1,036 features based on correlation. SIRIUS was a key software tool used in the non-targeted analysis workflow to help identify unknown chemical compounds, by generating potential molecular formulas and ranking potential chemical structures combined with MSFINDER. While the study did not find a single chemical driver, many compounds potentially related to breast cancer were present. Moreover, they successfully identified (confirmed with standards) novel drinking water contaminants. Notably, it's believed to be the first to report the presence of diphenyl sulfone (likely linked to paper recycling; positively correlated with ER agonism), and it also detected Benzothiazole-2-sulfonic acid (rubber vulcanisation accelerators) and Acetyl tributyl citrate (plasticiser used as a phthalate substitute; positively correlated with ER agonism). In addition, nine different PFAS were detected above their method quantification limits.

Keywords: drinking water, cancer, human, contamination, monitoring

Decoding the Chemistry of Space: How Untargeted Metabolomics is Mapping the ISS A recent study by researchers at UC San Diego has provided the most extensive look yet at the microbial and chemical landscape of the ISS. Using multi-omic sequencing and untargeted metabolomics, they created a comprehensive 3D map of the space station's surfaces. Only about 3% of the chemical features could be annotated by matching them against existing spectral libraries. This "dark matter" of unknown molecules required advanced computational tools. Our SIRIUS software was used to tackle this unknown territory, dramatically increasing the characterization of these molecules from 3% to nearly 97%! This allowed researchers to identify distinct "chemical hotspots" linked to different module functions, from corrosion inhibitors near exercise equipment to urinary metabolites near the hygiene unit. The findings provide a crucial baseline for designing future, healthier space habitats and highlight the power of advanced computational tools in exploring the unknown.

Keywords: microbiome, space, multiomics

Ethanol vs methanol: Safe off-site collection of human fecal samples To study the function of the gut microbiome, scientists often perform untargeted metabolomics on human fecal samples, along with genetic sequencing. Since more people are collecting samples at home, metabolomics experiments must adapt to ensure safe, high-throughput processing of large numbers of samples collected off-site. A 95% ethanol extraction method is part of the recently introduced high-throughput Matrix Method, is safer for non-scientific personnel to handle and can be used for bulk off-site sample collections. But does it yield comparable results to the more traditional 50% methanol extraction? A study by Zuffa and colleagues at University of California San Diego validates the 95% ethanol extraction to recover a comparable amount of metabolites from human faecal samples. Moreover, the faecal metabolome remains relatively stable for up to one week when stored in 95% ethanol at room temperature. This finding could reduce the high costs associated with refrigerated shipping for at-home collection studies. The researchers use SIRIUS for data processing. For metabolic features that could not be identified by matching against spectral libraries, the CANOPUS (Natural Product Classifier) tool within SIRIUS was employed to predict their molecular classes. It helped characterise the types of molecules uniquely recovered by each extraction method. CANOPUS predictions suggested that the 95% ethanol extraction recovered more oligopeptides and glycerolipids, whereas the 50% methanol extraction preferentially recovered small peptides and fatty acid conjugates. It was also used to predict the classes of metabolites that changed during the one-week storage period at room temperature, identifying small peptides and oligopeptides as among the most affected classes. Over 88% of metabolic features were detected at all time points (immediate, 1 day, and 1 week), and the method retained its power to distinguish between samples from different subjects. These findings demonstrate that the 95% ethanol extraction of the Matrix Method represents a valid, safer, and more economical alternative for large-scale gut microbiome research.

Keywords: CANOPUS, microbiome, multiomics, human

Multi-omics Analysis of Saccharina latissima Microbiome and Metabolome A recent study by a research team at Sorbonne Université provides new insights into the complex chemical and microbial interactions on the surface of the brown macroalga Saccharina latissima. Using a multi-omics approach, they investigated the ecological links between the alga's surface microbial communities (epimicrobiota) and its chemical profile (metabolome). Metabolomic analysis, employing liquid chromatography coupled to tandem mass spectrometry, identified diverse chemical compounds, including fatty acids, amino derivatives, amino acids, and naphthofurans. SIRIUS was one of the key computational tools (alongside GNPS) to determine the molecular formulas and putative structures of the unknown chemical compounds present on the alga's surface. The study established a link between the diversity of the microbial community and variations in the surface metabolome. Fungi and bacteria were identified as the primary drivers of these metabolomic variations. Two distinct microbial consortia were identified: one linked to bacterial groups and another to fungal groups, each associated with unique metabolites. The study suggests that certain metabolites are involved in chemical interactions between species and may contribute to the chemical defense of Saccharina latissima.

Keywords: marine, microbiome, ecology, chemical communication

Rethinking Plant Extraction: Green Solvents Unlock Bioactive Compounds A recent study published by researchers at Wageningen University and University of Parma investigated 20 different Natural Deep Eutectic Solvents (NADES) – a class of green, biodegradable solvents – for extracting bioactive molecules from Melissa officinalis (lemon balm). Green solvents are central to green extraction techniques, which are developed with the primary goal of minimising environmental impact and energy consumption while maximising the yield of extracted compounds. A key component of this research was a non-targeted, semi-quantitative metabolomics workflow. SIRIUS was employed for the comprehensive annotation of metabolites detected by high-resolution mass spectrometry, from molecular formula annotation, to structure elucidation and compound class prediction. The application of SIRIUS resulted in the putative annotation of 444 metabolites from the plant extracts. The researchers identified several known bioactive compounds that had never before been described in Melissa officinalis, effectively expanding the known chemical space of this medicinal plant. In addition, the semi-quantification of 385 metabolites made it possible to compare the extraction efficiency and selectivity of the different green solvents. They found that the thymol-menthol solvent performed with an efficiency comparable to conventional ethanol for broad-spectrum extraction. This establishes it as a viable, greener alternative with lower toxicity and a significantly improved greenness score for the sample preparation step. This shows that sustainability does not have to come at the cost of performance.

Keywords: environmental protection, plants

Anti-viral compounds in Caesalpinia mimosoides Researchers at Khon Kaen University, Thailand, discovered that a hydroethanolic extract of the plant Caesalpinia mimosoides is 3.35 times more effective against the influenza A virus than its traditional aqueous counterpart. To investigate why, they used SIRIUS to annotate the diverse range of bioactive compounds in this hydroethanolic extract and achieved high-confidence (level 2) annotations for 35 out of 48 bioactive metabolites. With the molecular structures confidently identified by SIRIUS, the team could perform molecular docking simulations and showed that the identified compounds likely help to inhibit influenza A virus by targeting two critical viral proteins.

Keywords: drug discovery, natural products, health, viruses

Constraining the molecular structure search space with chemical labeling Unlocking the chemical 'dark matter' in metabolomics is a persistent challenge. On average, less than 10% of features are confidently annotated, leaving a vast, uncharted chemical space. A research team led by Daniel Petras and Chambers Hughes at the University of Tübingen, in collaboration with the SIRIUS team, has developed a new workflow to address this challenge. Their new method, Multiplexed Chemical Metabolomics (MCheM), integrates online chemical labeling reactions directly into the liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow. This provides crucial structural information which is fed into SIRIUS via mzmine (mzio) to significantly constrain the molecular structure search space and boost annotation accuracy.

Keywords:

Identifying allergenic transformation products of tattoo pigments with SIRIUS Tattoo allergies are a growing concern as pigments in the skin are a source for allergens; often with delayed reactions. Naphthol AS pigments, including Pigment Red 5, are highly prevalent in allergic tattoo reactions. However, our understanding of how these pigments undergo biotransformation in human skin remains limited. Electrochemistry coupled to mass spectrometry mimics oxidative and reductive enzymes in the human body and has been a useful tool for simulating enzymatic biotransformation. But when applied to impure pigments, transformation products cannot be unequivocally assigned to the pigment itself, as they might originate from impurities. Unfortunately, as tattoo pigments are often manufactured for industrial purposes, they have purities of less than 90%, containing synthesis by-products and precursors. Researchers from University of Münster have developed an online-LC-EC-MS approach to overcome the challenge of impure pigment standards by separating pigments from impurities before simulating their metabolism, ensuring accurate assignment of transformation products. Using SIRIUS for data analysis, they have identified key transformation products (including quinones and primary aromatic amines) that may contribute to allergic reactions. SIRIUS 6 comes with integrated transformation product prediction by BioTransformer.

Keywords: biotransformation

Tackling the Opioid Detection Challenge with SIRIUS The rise of high-potency synthetic opioids like nitazenes presents a critical challenge in toxicology and public health. Their structural diversity, rapid emergence, and extremely low concentrations in biological samples make routine detection incredibly difficult. A recent study showcases the role of SIRIUS6 for confidently annotating nitazene metabolites from untargeted LC-HRMS data. The authors have identified multiple phase I and phase II metabolites, and major markers for enhanced detection. This research highlights the vital role of cutting-edge MSsoftware in addressing urgent public health challenges. The future of toxicology relies on highly sensitive untargeted analytical methods and the integration of MachineLearning for automated classification of novel analogues. Note that SIRIUS 6 now makes the detection of drug degradation products even easier with the integration of the BioTransformer.

Keywords: health, drugs, biotransformation, toxicity

Untargeted mass spectrometry is a powerful tool for analyzing the immense chemical complexity of natural environments. However, interpreting such large datasets remains a significant challenge. To overcome this, researchers have developed an innovative approach using SIRIUS that prioritizes chemical profiling over exhaustive identification. This method allows for more effective comparisons of (micro-)biomes, providing deeper insights into biochemical diversity across different environments.

Keywords: microbiome, biomarker, CANOPUS, chemical diversity, ecology, CSI:FingerID, monitoring

When we talk about antimicrobial resistance, the focus is often on bacteria. But multidrug-resistant fungi, like Candida auris, are an equally alarming threats; especially for immunocompromised patients. The challenges: - There are only three main types of common antifungal drug classes: Polyenes, Azoles, and Echinocandins. Moreover, the LC-MS/MS identification of polyenes is challenging as polyenes are prone to in-source fragmentation, vastly complicating the spectral analysis. - Rapid resistance development outpacing drug discovery: We must avoid wasting time on already known or undesirable compounds to accelerate the drug discovery process. Let's not underestimate this growing crisis! A research team led by Tim Bugni at the University of Wisconsin-Madison has developed a screening platform to discover antifungal drugs from natural sources. They combine liquid chromatography-tandem mass spectrometry (LC-MS/MS) for structural identification with yeast chemical genomics (YCG) for mechanism-of-action analysis and use SIRIUS to predict the structure of the antifungal agents. This combined approach efficiently identifies promising antifungal compounds while filtering out known or undesirable ones, significantly accelerating the drug discovery process. Some of the compounds identified are already the focus of more refined studies.

Keywords: fungi, drugs, drug discovery, health, infection

Agriculture has always been a dance with nature, requiring farmers to constantly adapt to changing conditions. One particularly promising method that has emerged over recent decades is push-pull technology, a strategy that uses nature's own defenses to protect crops and boost yields. Using SIRIUS, researchers uncovered metabolites in push-pull maize that enhance its natural defense against pests.

Keywords: crop protection, plants, herbivory, environmental protection, CSI:FingerID, CANOPUS, chemical communication

In a world where we're becoming increasingly conscious of what we consume, understanding the potential presence of unexpected extractables and leachables in our food and drinks is paramount. Alcoholic beverages are of particular concern due to their increased affinity and extended storage periods. A non-targeted approach to analysis is essential for uncovering both known and unknown contaminants in our drinks. By analysing fragmentation patterns, SIRIUS predicts chemical structures of unknowns to identify unexpected contaminants and ensure safety of our food.

Keywords: CSI:FingerID, food, health, contamination, extractables and leachables, polymers

Black apples are the result of late-stage microbial decomposition, mainly by Monilinia fructigena and Penicillium expansum, after falling to the ground. Both fungi produce various secondary metabolites that play roles in apple infection and also some of which have antifungal properties, influencing interactions and control of other microbes. However, fungal secondary metabolites in apples are not well understood. A research team at the Technical University of Denmark led by Thomas O. Larsen identified 3,319 unique chemical features in black apples, exceeding the abundance of microbial secondary metabolites compared to other environments. Only 6.4% of these secondary metabolites are known compounds. Due to the vast pool of unidentified secondary metabolites detected, they used SIRIUS and ZODIAC to predict molecular formulae, CSI:FingerID to annotate structures and CANOPUS to predict compound classes. They are now making efforts to isolate and characterize some of these key compounds for understanding their biological and ecological roles.

Keywords: food, plants, chemical diversity, CANOPUS, CSI:FingerID, ZODIAC, fungi, microbiome

Defense syndromes refer to sets of different chemical and physical traits that plants develop to protect themselves against threats like herbivores. These traits often work together to provide better protection than any single trait alone. Previous studies suggest that high variability in plant traits among closely related species enhance anti-herbivore defenses by reducing the number of shared specialized herbivores. Willows and their arthropod herbivores serve as an excellent model for studying trait syndromes and defense mechanisms, showcasing high intraspecific variability, diverse chemical defenses, and specialized herbivore interactions, which contribute to their exceptional species richness and complex defensive strategies. A research team led by Martin Volf at the Biology Centre of the Czech Academy of Sciences investigated several lowland willow species in central Europe to determine if their traits form detectable syndromes. To analyze constitutive chemical defences, they sampled plant leaves and analysed UHPLC-MS2 data using SIRIUS for molecular formula prediction, CSI:fingerID for structure prediction and CANOPUS for metabolite classification. They found that trait syndromes in willows likely result from a complex interplay of selection pressures and trade-offs, with herbivory being a significant factor, but additional factors also contribute to their formation, leading to chemical differentiation and niche segregation among closely related species.

Keywords: plants, defense, herbivory, CANOPUS, chemical communication, CSI:FingerID

Lipidomics is a branch of metabolomics, analyzing lipid species in complex mixtures. Gut microbiota's lipids play a key role in health, affecting immune responses and gut inflammation, with diverse structures and functions. Targeted and non-targeted lipidomics, combined with LC-MS, are effective for lipid analysis. Researchers at Helmholtz Zentrum München and Institut Pasteur led by Philippe Schmitt-Kopplin tested different reversed-phase LC columns to improve coverage of intestinal lipids. They addressed challenges in detecting certain lipids by testing 8 different mobile phase conditions on 5 columns. CANOPUS and CSI:FingerID were employed for lipid classification and the prediction of known and unknown features. They found that hybrid surface technology improves chromatographic parameters for lipid analysis, and ammonium acetate in ESI(-) or ammonium formate in ESI(+) increase lipid detection.

Keywords: lipids, microbiome, CANOPUS, CSI:FingerID

Studying how bacteria adjust their lipid composition under different environmental and nutrient stresses is crucial for understanding their survival and can inform the design of synthetic membranes for applications like filtration and drug development. In a study of Desulfatibacillum alkenivorans, researchers found that temperature changes and phosphorus deficiency influenced lipid diversity. Advanced analytical methods identified nearly 400 different lipids, revealing how these factors affected lipid composition. MS2 data analysis using Feature-Based Molecular Networking and SIRIUS showed that phosphorus limitation led to the creation of new lipids, such as glucuronosyl glycerols and butyramide cysteine glycerols, indicating a new bacterial survival strategy.

Keywords: lipids, bacteria

Fusarium graminearum, a fungal plant pathogen, affects cereal crops leading to significant economic losses due to reduced yields and contamination of grains with harmful mycotoxins. Synthetic fungicides can harm non-target organisms and promote fungal resistance. Natural products like plant extracts have shown antimicrobial properties against mycotoxin production. This study explores natural alternatives to chemical fungicides, focusing on grapevine byproducts rich in phenolic compounds, especially stilbenes. Using UHPLC–HRMS/MS analysis and metabolomics, they identified potent antifungal compounds, including several oligomeric stilbenes. Despite challenges in annotating stilbenes due to limited standards and databases, tools like CSI:FingerID and CANOPUS facilitated the dereplication process. Four significant oligomeric stilbenes were identified: cyphostemmin B, isohopeaphenol, another stilbene tetramer, and a trimer putatively annotated as vaticanol G.

Keywords: CSI:FingerID, CANOPUS, fungi, plants, pathogens, toxicity, agriculture, food

Cyanobacteria are found worldwide living in various environments like freshwater, land, and sea. Cyanobacterial blooms in freshwater sources harm water quality by reducing oxygen levels and releasing harmful toxins. These toxins, known as cyano-metabolites, can enter water treatment plants if not treated properly, potentially contaminating drinking water. Researchers at Eawag developed a method for efficient high-throughput screening of how different cyano-metabolites interact with ozone during water treatment. Since no spectral libraries exist for most cyano-metabolites, they used SIRIUS and MetFrag for compound annotation. Studying the fate of 31 cyano-metabolites, they found that some may be effectively removed by ozonation, while others may require hydroxyl radicals for degradation.

Keywords: bacteria, wastewater, drinking water, toxicity, contamination

Cholesterol is essential for all animal life, being an essential structural component of animal cell membranes, also implicated in cell signaling processes, and a precursor for the biosynthesis of steroid hormones, bile acid and vitamin D. But elevated levels of cholesterol in the blood lead to atherosclerosis which may increase the risk of heart attack, stroke, and peripheral artery disease. Recent evidence links cardiovascular disease to an altered gut microbiome, but understanding the mechanisms has been challenging due to a lack of comprehensive multi-omic data. To address this researchers from several US American universities led by Ramnik J. Xavier at Harvard Medical School conducted a detailed study using stool metagenomics and metabolomics. The untargeted metabolomics data was annotated using CSI:FingerID. They found Oscillibacter species in the gut microbiome may help lower cholesterol levels, potentially benefiting heart health, and further used various methods to explore their cholesterol-metabolizing abilities, such as glycosylation and dehydrogenation.

Keywords: human, diseases, microbiome, bacteria, metabolic pathways, biotransformation, food

Thawing permafrost, caused by climate change, releases stored carbon into the atmosphere, accelerating global warming. The enzyme latch hypothesis suggests that low-oxygen conditions in wetlands slow down enzymatic polyphenol degradation and carbon release. But are oxygen-dependent phenol oxidases really the only enzymes that microbial communities have in their arsenal? Or should we perhaps take a closer (metatranscriptomic and metabolomic) look at the microbially catalysed carbon cycle?

Keywords: bacteria, climate change, environmental protection, biotransformation, CSI:FingerID, CANOPUS

Ketamine is known for its dual role as an anesthetic and an emerging antidepressant. Despite its long-standing clinical use, the metabolic pathways and pharmacokinetics of ketamine remain poorly understood. The anesthetic and analgesic properties of ketamine are primarily mediated through its antagonism of the N-methyl-D-aspartate (NMDA) receptor. Different mechanisms have been suggested for ketamine's antidepressant effects in the brain. A research team around Daniel Globisch and Uppsala University and Iben Lundgaard at Lund University has investigated ketamine metabolism and the distribution of ketamine metabolites in the pig brain using SIRIUS. They detected and identified numerous phase I and phase II metabolites of ketamine, including five metabolites that have been described in vivo for the first time. Moreover, they found two brain regions that differed in the distribution of ketamine metabolites from the other ten regions; both regions are linked to the clearance of metabolites from the brain. Understanding how ketamine traverses the blood-brain barrier holds promise for optimizing treatment strategies and enhancing patient outcomes.

Keywords: human, drugs, drug discovery, neuroscience, diseases, biotransformation

When examining interactions between fungi and various biocontrol species, researchers found the growth of the organisms was halted and distance inhibition was observed. Morphological changes in the fungal hyphae indicate a metabolic reprogramming within the organisms, hinting at the potential formation of secondary metabolites during these interactions. To understand the chemical changes during these confrontations, they used LC-MS/MS analysis and revealed the production of several metabolites that were only synthesized when the fungi and bacteria were in confrontational settings, suggesting a unique metabolic response to these interactions. Using SIRIUS, they found that many of those metabolites belong to the fatty acyls.

Keywords: fungi, bacteria, bioactivity, biocontrol, chemical communication, CANOPUS, CSI:FingerID

Microalgae, such as Spirulina, are promising sources of sustainable nutrition with rich nutrient profiles. Ensuring consistent quality of microalgae as dietary supplements requires a quality control method reporting about their chemical composition. Mass spectrometry-based metabolomics coupled with SIRIUS helps identifying primary and secondary metabolites with potential health benefits, including free fatty acids, polar lipids, and pigments.The study uncovered significant differences in metabolite abundance and composition among Spirulina, Chlorella, and Amphora. The analysis revealed significant variations in the metabolome of Spirulina samples attributed to differences in cultivation settings. This highlights the pressing need to optimize cultivation conditions to ensure consistent quality of microalgae as dietary supplements.

Keywords: bacteria, human, environmental protection, food, CSI:FingerID, marine

The use of new psychoactive substances derived from ketamine is not commonly reported in France. The researchers encountered a patient who regularly consumed GHB, 3-MMC, and methoxetamine and experienced a loss of consciousness in a chemsex context. The patient was admitted to the intensive care unit and had a rapid and favorable recovery. To investigate the chemicals responsible for the intoxication, the researchers conducted a comprehensive targeted and untargeted LC-MS/MS analysis using various samples collected from the patient (plasma, urine, hair). The results confirmed that the patient had been exposed to multiple drugs, including a new psychoactive substance called deschloro-N-ethyl-ketamine (O-PCE), which has been sold online as a designer drug. Using a molecular network-based approach and SIRIUS, the researchers annotated 27 O-PCE phase-I and phase-II metabolites in the patient's plasma and urine samples and proposed a metabolic pathway. Several of the phase II O-PCE metabolites were identified for the first time in this study.

Keywords: drugs, metabolic pathways, biotransformation, human, CSI:FingerID

Decomposition is a vital process that sustains life on our planet by recycling nutrients and enriching ecosystems. Microbial decomposers, including bacteria and fungi, play a crucial role in breaking down organic matter into simpler compounds. However, there's still much to uncover about how these microbial communities assemble, interact, and function within ecosystems. Jessica L. Metcalf and her team at Colorado State University delved into the microbial ecology of human decomposition across different climates, geographic locations, and seasons. By monitoring decomposition processes in various settings, they aimed to uncover universal trends in microbial decomposer communities. Using metagenome assembly and metabolomics analysis, they examined - the universal microbial decomposer network that assembles in response to mammalian remains - how the cadaver-derived nutrient pool changes during decomposition process (using ZODIAC), and - whether this microbial community change can be used for predicting time since death for forensic purposes.

Keywords: bacteria, fungi, ZODIAC, microbiome, biotransformation

Antibiotics are crucial for fighting bacterial infections, but the rise of antibiotic resistance poses a serious threat to public health. Beyond healthcare, the presence of antibiotic residues in wastewater exacerbates the problem. Conventional treatment methods often fall short in adequately removing these compounds, perpetuating resistance. Biological processes, such as biotransformation by fungi, have emerged as promising alternatives. Researchers investigated the potential of fungi to transform antibiotics, using SIRIUS and CSI:FingerID to identify degradation products.

Keywords: biotransformation, drugs, antibiotics, fungi, environmental protection, wastewater

Microorganisms play a crucial role in shaping ecosystems through their metabolic activities, yet much of their chemical potential remains untapped in modern metabolomics experiments. Less than 1% of annotated molecules in untargeted metabolomics studies are classified as microbial, leaving a vast expanse of the microbial chemical space unexplored. microbeMASST is leveraging a curated database of >60,000 microbial monocultures. Users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. These MS/MS spectra can then be processed with SIRIUS and CANOPUS to tentatively annotate the metabolites and identify their chemical classes. microbeMASST and SIRIUS help to uncover microbial metabolites without any prior knowledge, expanding our understanding of microbial contributions to various ecosystems.

Keywords: microbiome, CANOPUS, CSI:FingerID, bacteria, fungi

This study investigates the relationship between dietary patterns, plasma metabolites, and colorectal cancer (CRC) risk. By examining the metabolite profiles using SIRIUS, they found that certain metabolites reflecting alcohol intake were associated with increased CRC risk, while others indicative of fiber, wholegrain, and fruit and vegetable consumption were linked to decreased risk.

Keywords: food, cancer, human

The microbial diversity and metabolite production of the tropical ascidian Eudistoma vannamei reveals its role as a holobiont rich in secondary metabolites. An omics approach was used to study the ascidian as a holobiont, including analyzing microbial diversity through 16S rRNA gene sequencing and metabolite production using mass spectrometry-based metabolomics. The in silico chemical classification was obtained from CANOPUS. The study identified various compounds, including phospholipids, amino acids, and pyrimidine alkaloids, in both the ascidian tissue and isolated bacteria.

Keywords: marine, CANOPUS, animals, bacteria, microbiome

Despite being one of Earth's most abundant polymeric organic compounds, lignin is often considered a lower-value byproduct in industrial processes. Converting lignin into valuable chemicals or biomaterials requires a thorough structural characterisation of depolymerised products. This non-targeted analysis method involving 2D liquid chromatography and high-resolution tandem mass spectrometry uses SIRIUS in versatile ways to unravel the complex structures of depolymerized lignin.

Keywords: environmental protection, plants, material science

The microbiome associated with the eelgrass Zostera marina, especially leaf epiphytes, produces powerful broad-spectrum antibiotics, including Streptomyces sp. strain 131, which outperforms some control drugs. These microbes demonstrate significant activity against common aquatic, human, and plant pathogens, emphasizing the potential of seagrass microbiomes in mitigating the abundance of harmful pathogens in seawater. The study investigates the rich secondary metabolite composition by untargeted metabolomics using SIRIUS with CANOPUS and CSI:FingerID. The findings contribute to our understanding of the microbial and chemical ecology of seagrasses, offering insights that could aid future seagrass conservation and management strategies, particularly in the context of climate change and its anticipated impact on infectious diseases.

Keywords: CANOPUS, CSI:FingerID, microbiome, marine, antibiotics, plants, pathogens

Flame retardants are chemicals added to products for fire resistance, but they can be released into the environment. Honey contamination has been suggested as an indicator of pollution. The study used LC-QTOF-MS to analyze honey samples from urban and rural areas and found no significant difference in flame retardant levels. Tris(2-butoxyethyl) phosphate and triphenyl phosphate were detected at trace concentrations in a targeted screening approach. A non-targeted screening method using SIRIUS further identified tris(2-chloropropyl) phosphate and other compounds yet to be validated.

Keywords: environmental protection, food, contamination

This study explores the phytochemistry of Eclipta alba cultivated in the center-Val de Loire Region identifying coumestans like demethylwedelolactone and wedelolactone along with other phenolic compounds as key contributors to its anti-inflammatory antioxidant and novel anti-collagenase activities. The study involved extracting aerial parts of the plant with ethanol fractionating the extract and utilizing advanced analytical techniques such as HRMS/MS and NMR for compound identification. For the formulae previously non-identified in E. alba the MS/MS data were processed with SIRIUS. The findings suggest that Eclipta alba from this region holds promise as a natural and effective anti-aging ingredient for cosmetic applications.

Keywords: pharmacology, cosmetics, plants

This study investigates the formation of secondary brown carbon (BrC) through aqueous-phase reactions of α-dicarbonyls with ammonium or amines, shedding light on previously unknown chromophores. Using SIRIUS+CSI:FingerID, they identify 180 chromophores, with 155 of them being newly discovered, revealing their significant contribution to light absorption in bulk BrC. Additionally, the study highlights the pH-dependent effects on BrC chromophore formation and transformation, providing valuable insights for future research on aqueous-phase BrC formation.

Keywords: atmosphere, CSI:FingerID, environmental protection

The ectomycorrhizal symbiosis between trees and Tricholoma vaccinum, a basidiomycete fungus, is mutually beneficial. Tricholoma vaccinum is mainly observed with fruiting bodies occurring under spruce and rarely found under pine. The interaction with the compatible host Picea abies is faster and more complete compared to Pinus sylvestris. Stable symbiotic associations between fungi and plants require specific communication and overcoming plant defenses. To test the specific role of volatiles, trees were exposed to the complete volatilome of the fungus versus the fungal volatilome reduced for terpenoids. The trees' phytohormone and metabolome responses to the early signals transmitted through volatiles were scored. Structural proposals for individual metabolites were determined using SIRIUS. The study found a molecular explanation for the longer time needed to establish the low-compatibility interaction between the ectomycorrhizal fungus Tricholoma vaccinum and pine.

Keywords: CSI:FingerID, CANOPUS, ZODIAC, COSMIC, plants, fungi, chemical communication

Our skin, beyond being a physical barrier, hosts a diverse community of microorganisms known as the skin microbiota. Biotics have gained attention for their potential to enhance the skin's health, though their exact mode of action is still unclear. MS-based metabolomics has emerged as a powerful tool to characterize the chemical composition of the skin surface and correlate it with microbial communities. Using CSI:FingerID, researchers identified changes in the skin metabolome that are more pronounced than changes in the microbial composition, suggesting that even subtle shifts in microbial abundance can lead to significant effects on the skin.

Keywords: cosmetics, microbiome, bacteria, CSI:FingerID, human

The methanogenic archaeon Methanosarcina barkeri has the capability to reduce naturally occurring iron oxides, including amorphous iron, magnetite, and hematite, under conditions resembling the methanogenic zone in aquatic sediments. This study suggests that methanogens, which are typically associated with methane production, can also play a role in microbial iron reduction. To learn more about the relationships and structures of the metabolites in the cultures, a molecular network was created in GNPS and SIRIUS, with CSI:FingerID and CANOPUS, was used to annotate compounds. They identified a compound with a similar structure to hydroxyindole, that plays a role in the promotion of iron reduction by electron shuttles. Adding dissolved phenazines as electron shuttles to the media with iron oxides increased iron reduction and inhibited methanogenesis almost completely. This studysheds new light on the interplay between microbial iron reduction and methane emissions in these environments.

Keywords: archaea, marine, environmental protection, CSI:FingerID

This study explores the chemical composition of three Ficus species using molecular networking. The goal is to understand their phytochemistry and chemotaxonomy. 90 metabolites were identified using SIRIUS + CSI:FingerID and MetFrag, with phenolic acids being the most abundant. Different species showed variations in metabolite classes, and this matched their genetic differentiation. F. drupacea demonstrated strong inhibition of H. pylori, making it a potential candidate for medicinal use.

Keywords: plants, CSI:FingerID, CANOPUS, pharmacology, drug discovery

Migraine is a common, polygenic disorder characterized by severe headaches, often treated with triptans (serotonin receptor agonists). However, triptans work for only about 60% of people, and their mechanisms are unclear. To uncover these mechanisms, this study (untargeted) metabolomics to find changes initiated by the migraine attack and/or the treatment and integrated with transcriptomics to map molecular mechanisms. Using SIRIUS and CSI:FingerID they identified three metabolites differentially expressed after treatment: cortisol, sumatriptan, and glutamine.

Keywords: human, CSI:FingerID, CANOPUS, pharmacology, drugs, diseases

Cathodic protection is used to prevent corrosion in marine environments by sacrificing zinc or aluminium-zinc-indium alloy anodes. Little is known about their effects on marine life. This study examined their impact on oysters and found that zinc anodes influenced 16 metabolites and aluminium-zinc-indium anodes two. Using targeted MS/MS of the discriminant metabolites and using SIRIUS+CSI:FingerID for annotation, they found that these metabolites play roles in various biological processes, from energy metabolism to defense mechanisms.

Keywords: marine, environmental protection, CSI:FingerID, CANOPUS, material science, animals

Thiacloprid is a first-generation, widely used, neonicotinoid insecticide. Its persistence in the environment and potential adverse effects on human health have raised significant concerns. Understanding its impurity profile is crucial for assessing its environmental impact and potential risks to human health due to exposure. Regulatory authorities require comprehensive impurity profiling of pesticides like thiacloprid to ensure their safety and to set acceptable limits for impurities. So far, there has been no reported impurity profiling of thiacloprid. This study employs liquid chromatography-high resolution mass spectrometry (LC-HRMS) and SIRIUS for de novo identification and categorizes eighteen impurities in thiacloprid, demonstrating an efficient approach to address the challenge of identifying structurally related impurities in pesticides.

Keywords: crop protection, profiling, CSI:FingerID, ZODIAC, environmental protection, toxicity

Mammalian hibernators experience significant metabolic changes during their hibernation cycle. Researchers studied the metabolic profile of white adipose tissue in thirteen-lined ground squirrels during active and hibernating periods. They analyzed various compounds in the tissue annotated with CSI:FingerID and found distinct metabolic patterns at different hibernation stages. Notably, they observed elevated levels of beta-hydroxybutyrate (BHB) and BHB-carnitine conjugate during torpor, suggesting that white adipose tissue contributes to increased circulating BHB levels during hibernation. White adipose tissue plays a crucial role in regulating metabolism throughout the hibernation cycle.

Keywords: animals, CSI:FingerID

Two new ecdysteroids, along with four known ones, were isolated from the Korean plant Ajuga spectabilis. Their structures were determined through MS and NMR. SIRIUS was used for compound annotation and CANOPUS compound class predicition. Via machine learning the authors predicted the receptor, supported by molecular docking results. Testing on UVB-exposed HaCaT cells showed inhibited expression of the receptor which is of potential therapeutic benefit to skin aging.

Keywords: CANOPUS, cosmetics, CSI:FingerID, plants

Formulation ingredients are a mixture of molecules that help to enhance the solubility of the active substance in commercial pesticides. So far, a relatively low attention is given to their analysis and fate tracking in the environment. In this study, these ingredients have been analyzed using LCMS-based screening and metabolite annotation with SIRIUS and CSI:FingerID of herbicides applied to soil. The study reveals distinct spectral and chromatographic patterns in the analysis, including amplified adducts, double-charged ions formation, and changes in chromatographic profiles.

Keywords: herbivory, crop protection, CSI:FingerID, plants, soil, environmental protection

Marine prokaryotes offer a rich source of untapped bioactive secondary metabolites for drug discovery, as demonstrated through genomic analysis. They analyse the secondary metabolite production of bacterium A. muelleri DSM 19832 using UPLC-QTOF-MS/MS and tentative SIRIUS annotations. This study also reveals that the vast majority of the biosynthetic potential remains unexplored, highlighting the significant promise for discovering novel marine prokaryotic natural products with pharmaceutical applications.

Keywords: bacteria, CSI:FingerID, marine, drug discovery, chemical diversity

Plants rely on cross-resistance traits evolved through co-evolution to defend against diverse enemies, but the cross-resistance potential of native plants facing new invaders is poorly understood; for instance, the emerald ash borer (EAB) and ash dieback (ADB) pathogen threaten European ash trees. Using an untargeted approach, in this study the specialized metabolomes of ADB-resistant and ADB-susceptible as well as EAB-infested and uninfested ash trees were compared. For feature identification, SIRIUS utilizing CSI:FingerID and CANOPUS were used. They found that EAB performed better on ADB-susceptible genotypes and linked this to differences in phloem chemistry. The study suggests that ADB-resistant ash types could mitigate both ADB disease and EAB losses, benefiting the long-term stability of these key trees.

Keywords: CANOPUS, CSI:FingerID, defense, fungi, herbivory, pathogens, plants

This study investigates the chemical composition and anti-inflammatory properties of Urospermum picroides, a wild edible plant that can grow in harsh environments. Using SIRIUS and CSI:FingerID, they identified 77 metabolites in the plant extract, including 12 new sesquiterpene-amino acid conjugates. They also found that the extract reduced inflammation in a cell model by modulating cytokine secretion. The results suggest that U. picroides could be a valuable source of bioactive compounds for food and health applications.

Keywords: CSI:FingerID, food, plants, pharmacology

Energy-cane is a hybrid of sugarcane and differs in fiber, sucrose, and productivity. This study explored how the diurnal cycle impacts carbohydrate and metabolite production in both. Using CANOPUS compound class annotations, a correlation network analysis grouped metabolites with similar diurnal abundance profiles into modules. Results highlight fluctuations in sugars and metabolites, showcasing distinct growth strategies. Energy-cane's mature parts contain abundant starch, and certain growth-related pathways are more active in it. Metabolites linked to biomass production are more abundant in energy-cane. This insight aids in potential more efficient breeding efforts.

Keywords: energy, food, CANOPUS, ZODIAC, plants

Untargeted metabolomics approach using CSI:FingerID and CANOPUS to investigate willow species for different chemical profiles depending on their elevation level and evolutionary history. Elevation affects chemical variation among species more than chemical richness within species, and highland and lowland willows have different trends in metabolite concentration and diversity

Keywords: CANOPUS, herbivory, plants, CSI:FingerID

This study examined the red alga Asparagopsis armata's life cycle stages, including gametophytes, tetrasporophytes, and female gametophytes with cystocarps. The analysis revealed fluctuating halogenated compounds and different antibacterial activities among the stages. The tetrasporophyte stage displayed the highest antibacterial activity and a more diverse bacterial community. Using SIRIUS, highly halogenated compounds were identified as potential contributors to the observed antibacterial effects.

Keywords: marine, bacteria, plants, drug discovery, pharmacology, halogenated compounds

Metal nanoparticles are particles that range in size from 1 to 100 nanometers and are made of metals such as gold, silver, iron, copper, and others. They have a broad variety of applications in computing, optics, cosmetics, food industry, medicine, and water treatment, among others. Silver nanoparticles, known for their antimicrobial properties, are effective for remediating contaminated waters. Plant extracts are used as reducing agents for environmentally friendly silver nanoparticle synthesis. To improve this synthesis, identifying the biomolecules involved in the process is crucial. UHPLC-QTOF-MS and SIRIUS identified the key phenolic compounds involved in the silver reduction.

Keywords: CSI:FingerID, material science, nanomaterials, drinking water, plants, environmental protection, contamination

Australian native fruits possess rich and unique phytochemical profiles due to the intense climatic conditions of the region. In this study, the antiproliferative activity of water and ethanol extracts from Australian native plums was evaluated against MCF7 breast adenocarcinoma cells. Kakadu plum extracts showed the most potent antiproliferative effects. The active extracts induced apoptosis in the cancer cells but did not increase reactive oxygen species production. Metabolomic identification with CSI:FingerID and CFMID revealed the presence of potential anticancer compounds.

Keywords: cancer, CSI:FingerID, human, pharmacology, food, plants, drug discovery

Brown carbon, arising from the combustion of organic matter, exerts a significant influence on atmospheric radiation and global climate. To fully comprehend its impact on atmospheric processes, a thorough characterization of the light-absorbing brown carbon molecules is imperative. Using CSI:FingerID, researchers have successfully annotated 100 brown carbon chromophores, 33 of which have never been reported before. Through the identification and characterization of these chromophores in diverse atmospheric samples, we gain invaluable insights into their origins, behavior, and the profound implications they have on radiative forcing, cloud formation, and the intricate web of global climate change.

Keywords: atmosphere, climate change, CSI:FingerID

Metabolome composition of mature and immature seeds from different cereal and leguminous plants. They used Sirius + CSI:FingerID to identify 146 metabolites from various classes, including some that were reported for the first time. They found that sugars were dominant in mature seeds, while oxylipids were dominant in immature seeds. The study also assessed antioxidant activity and found that mature barley seeds had the highest activity.

Keywords: food, plants, antioxidation, CSI:FingerID

The process of domesticating crops reduces the variety of genes involved in different metabolic functions, particularly those related to specialized metabolism. While this reduction in genetic diversity is well-known, the decrease in diversity at the metabolite level has not been adequately studied. This study used untargeted metabolomics, molecular networking in combination with SIRIUS CSI:FIngerID annotation, and information theory, and found that domesticated common bean varieties have lower metabolic diversity and specialization compared to their wild counterparts, indicating a shift towards central metabolism during domestication.

Keywords: CSI:FingerID, food, plants

The study explored the use of phospholipid vesicles to formulate a hydro-ethanolic extract from <i>Ceratonia siliqua</iripe pods, which exhibited antioxidant properties due to the presence of biologically active compounds identified by liquid chromatography-mass spectrometry. Compounds were identified using SIRIUS + CSI:FingerID. The vesicles showed favorable characteristics and biocompatibility, making them a potential topical formulation for therapy with antioxidant activity.

Keywords: CSI:FingerID, plants, cosmetics, bioactivity, antioxidation

Plants produce diverse chemical defenses with varying effects on different insect herbivores. Tailoring herbivore-specific responses can enhance plant defense efficiency. This study investigates how induced plant responses relate to herbivore species, order, feeding guild, and specialization, by analyzing changes in volatile and nonvolatile leaf metabolites following herbivory. Using SIRIUS, CSI:FingerID and CANOPUS, they detected 64 compounds with untargeted metabolomics when analyzing small nonvolatile leaf metabolites. Insect presence primarily influenced the variation in nonvolatile leaf metabolites, while herbivore identity had little impact. Most nonvolatile metabolites were downregulated, suggesting a resource shift in response to herbivory.

Keywords: CANOPUS, CSI:FingerID, chemical diversity, defense, herbivory, plants

This study focuses on analyzing the nutritional components of coconut flesh and exploring the molecular mechanisms behind the biosynthesis of amino acids, polyamines, and lipids in different coconut subspecies. The researchers conducted a comprehensive analysis using multi-omics approaches, including metabolome and transcriptome analyses. Employing SIRIUS CSI:FingerID and Compound Discoverer, they detected and identified a total of 52 amino acids and derivatives, 8 polyamines, and 158 lipid metabolites in coconut flesh.

Keywords: CSI:FingerID, food, plants

Stable isotope labeling serves as a detection strategy to distinguish biologically relevant features from background signals. In this case study, a total of 37,000 features were detected, out of which 2,119 features (5.8%) were credentialed as biologically derived. Successful annotation was achieved for 198 metabolites at Level 2A using the MS2 spectral database, and additional metabolites were annotated at Levels 3 and 4 using MetFrag and CSI:FingerID.

Keywords: CSI:FingerID, fungi, food

In the world of microbiology, there's an ongoing battle between different bacterial species competing for survival and dominance. However, under certain conditions, two species can actually thrive together in a dual-species biofilm. The cooperation between P. aeruginosa and S. aureus in cystic fibrosis leads to increased disease severity. But so far, only little is known about the chemical communication mechanisms between those bacteria. CSI:FingerID identifies a metabolite that could be related to the increased pathogenesis of this dual-species biofilm in cystic fibrosis.

Keywords: diseases, bacteria, chemical communication, CSI:FingerID, pathogens, infection, human

Ginger has been used as consumed food spice and folk medicine in daily life for thousands of years in various regions of the world. It is known to exhibit health-promoting effects due to its considerable antioxidation activity. This bioinformatic workflow was developed to generate activity labelled molecular networking (ALMN) to generate antioxidation active molecules profile of Ginger. SIRIUS + CSI:FIngerID was used to conduct high confidence structure annotations of antioxidation active molecules. Consequently, 48 molecules were prioritized as antioxidation active molecules from 11,720 metabolite molecules of Ginger in a systematical way.

Keywords: antioxidation, CSI:FingerID, food

Endophytic bacteria are capable of controlling fusarium wilt disease and promoting the growth of tomato plants. Bioactive secondary metabolites produced by the bacteria take part in their biocontrol activity. Sriwati et al explored those metabolites using molecular networks that were annotated through SIRIUS and CSI:FingerID: Clusters were annotated by compound class and many possible structures of secondary metabolites produced by these bacteria were elucidated. Although the active compounds of the bacterial extracts could not be identified, many compounds have the potential to exhibit antibacterial or antifungal activity (containing azole or allylamine subunits).

Keywords: bacteria, crop protection, CSI:FingerID, plants, food, bioactivity

Researchers are searching for natural antimicrobial agents due to the prevalence of multidrug-resistant pathogens. A rare actinobacteria strain was isolated from Egyptian soil and identified as Amycolatopsis keratiniphila DPA04. Its crude extracts were found to have antimicrobial activity against Gram-positive bacteria. Analysis of the crude extracts using UHPLC-QTOF and SIRIUS + CSI:FingerD led to the identification of 45 metabolites of different chemical classes. ECO-0501 was identified in the cultures with significant antimicrobial activity. Molecular docking studies confirm that it is a promising candidate as MATE (multidrug efflux pump) inhibitor. Natural products from this strain could be useful therapeutic tools for controlling infectious diseases.

Keywords: antibiotics, bacteria, CSI:FingerID, pharmacology, pathogens, drug discovery, soil

This study investigates Phragmites australis, a wetland grass, to understand how metabolites contribute to plant invasion success.They analyzed the plant lipidome and metabolome using SIRIUS and CSI:FingerID to predict molecular structures, which in turn were used to classify compounds using ClassyFire and NPClassifier. Using Random Forests, they identified informative features that distinguished five lineages: European native, North American invasive, North American native, Gulf, and Delta. The study found that each lineage had unique phytochemical fingerprints, with some overlap between North American invasive and native lineages. The results suggest that metabolomic evenness may be a critical trait within plant species.

Keywords: biodiversity, CSI:FingerID, invasive species, plants

The use of sunscreen is essential for public health, but the ultraviolet filters in these products can harm marine organisms, including coral. Butyl methoxydibenzoylmethane (BM) is a UV filter that has already been tested for coral inflammation which is not caused by BM. However, coral exposed to BM is subject to a metabolomic shift. Exploring the metabolism of corals exposed to increasing concentrations of BM, SIRIUS+CSI:FingerID identified two carotenoids that are required for the formation of photosynthetic pigment–protein complexes of the thylakoid membrane. The decrease in the relative concentration of these two carotenoids might be indicative of an alteration in the photosynthetic capacity of the coral. We need to evaluate the levels of BM contamination in the reefs and surrounding waters of anthropized areas to assess whether BM could contribute locally to coral bleaching.

Keywords: animals, CSI:FingerID, toxicity, marine, environmental protection, contamination

Neonatal dried blood spots are not only important for newborn screening but also a powerful source for investigating the potential metabolic etiologies of various diseases using untargeted LC-MS-based metabolomics. So far it is unclear whether the metabolites in those samples remain stable in storage. CSI:FingerID and CANOPUS help to investigate the stability of metabolites and classes of molecules.

Keywords: CANOPUS, CSI:FingerID, human, monitoring

The invasive tree species Miconia calvescens threatens the biodiversity of French Polynesia. This study investigated the impact of M. calvescens on the rhizosphere of six plant species at both the seedling and tree stages. They used metabarcoding and metabolomics to study the diversity of soil organisms and secondary metabolites. Compounds were identified using SIRIUS+CSI:FingerID. The results showed that M. calvescens had a specific association with microeukaryotes of the Cryptomycota family at the tree stage, and this family was positively correlated with the terpenoids found in the soil. The study suggests that these molecules might contribute to the success of M. calvescens as an invasive species.

Keywords: bacteria, biodiversity, CANOPUS, CSI:FingerID, invasive species, plants, soil

Alzheimer's disease is a neurodegenerative condition that affects cognitive function and is expected to triple in the US by 2060, with treatment costs projected to rise to over $500 billion annually. Cholinesterase inhibitors can improve cognitive decline by increasing the neurotransmitter acetylcholine, but they also have side effects such as bradycardia, nausea, stomach pain, anorexia, and diarrhea. Endophytic fungi live inside plant tissues without harming their host and produce a variety of bioactive secondary metabolites which are a promising source of novel cholinesterase inhibitor candidates. In this study, metabolites of anAspergillus niveus ethyl acetate extract were annotated using SIRIUS and CSI:FingerID. While the isolated compounds displayed only moderate activity against cholinesterases, structurally related metabolites yielded considerable anticholinesterase activities and are promising leads for developing new potent cholinesterase inhibitors.

Keywords: diseases, CSI:FingerID, pharmacology, fungi, bioactivity, human, drug discovery

Liverworts are chemically diverse plants with unique cell organelles responsible for the synthesis and storage of specialized metabolites. Untargeted metabolomics was used to analyze the metabolic stress response of liverworts without isolating individual metabolites. CANOPUS classified the affected compounds and helped to map the biochemical pathways of the unique stress response of liverworts compared to vascular plants.

Keywords: CANOPUS, CSI:FingerID, plants, stress response, ZODIAC, toxicity, chemical diversity

Morrison et al. used Sirius and CSI:FingerID to describe the metabolome of the invasive Guinea grass for the first time, identifying 37 unique secondary metabolites. They compared the effect of the known allelochemical 2HPAA with that of the whole-plant chemical extract, which had significantly stronger effects than pure 2HPAA.

Keywords: biodiversity, plants, invasive species, CSI:FingerID

The strategy of ATP spilling, which involves degrading ATP into ADP to enhance metabolic activity and productivity, has been rarely implemented in Streptomyces species. However, antibiotic production by these microorganisms is known to be triggered in conditions that correlate with low ATP content. Researchers cloned the gene for the DX protein, which dephosphorylates ATP into ADP, and introduced it into Streptomyces albogriseolus/viridodiastaticus. used LC/HRMS2 to analyze the molecules produced by the resulting strain A37 and a control strain A36. Molecular formulas of compounds of interest were predicted with SIRIUS and class annotation was confirmed with CANOPUS. The study demonstrated that DX can be an efficient tool for enhancing specialized metabolic pathways in Streptomyces, potentially leading to the discovery of novel bioactive molecules.

Keywords: pharmacology, antibiotics, bacteria, CANOPUS, stress response, bioactivity

Marine microorganisms offer a rich source of bioactive compounds with unique structures and remarkable biological activity. This makes them an important resource for the search for new therapeutic compounds, which is one of the most pressing challenges of our time. To narrow down the search to the most promising microorganisms, SIRIUS is nearly doubling the number of natural products annotated to estimate the chemical potential of microbial extracts.

Keywords: CANOPUS, bacteria, CSI:FingerID, toxicity, pharmacology, marine, bioactivity, chemical diversity, drug discovery

This study investigated the potential of four citrus juices to improve herbal therapy against paracetamol-induced liver toxicity. The juices were analyzed for their metabolites, particularly phenolic compounds, and exhibited antioxidant activity. Metabolites were tentatively identified using Sirius and GNPS. In a rat model of paracetamol-induced liver injury, the concomitant administration of citrus juices effectively recovered liver injury, likely due to interactions between certain identified metabolites and specific cytochrome P450 isoforms. The most promising compounds in the docking study were hesperidin, fortunellin, poncirin, and naringin. This food-drug interaction may overcome paracetamol overdose-induced hepatotoxicity.

Keywords: drugs, food, plants, toxicity

Fusarium verticillioides threatens maize production globally by infecting kernels and producing harmful fumonisins. Maize breeding aims to reduce contamination. This metabolomic study on genetically related inbreds with varying resistance levels revealed relevant pathways involved in resistance. Membrane lipid homeostasis, methionine metabolism, and indolacetic acid conjugation were important differentiators. Significant metabolite features were annotated using SIRIUS and CSI:FingerID. Specific metabolites like spermidine and isoquinoline alkaloids showed promise as potential selection traits to improve resistance and reduce fumonisin accumulation, pending further validation.

Keywords: CSI:FingerID, crop protection, defense, food, fungi, plants, infection

This study investigated the potential protective effect of extracts from Artemisia absinthium (wormwood) on the stomach. They tested two extracts obtained through hot and room temperature maceration of A. absinthium aerial parts in rats and found that the room temperature extract was more effective. It reduced gastric ulcers and prevented inflammation. The extract seemed to maintain the stomach's protective barrier. Using SIRIUS they putatively identified with a high level of confidence (COSMIC score at least 80%) eight main peaks as tuberonic acid glycoside, rupicolin, 2-hydroxyeupatolide, yangabin, sesartemin, artemetin, isoalantodiene, and dehydroartemorin. These findings support the traditional use of A. absinthium for stomach problems.

Keywords: pharmacology, bioactivity, plants, COSMIC, CSI:FingerID, food

This study explores the effects of FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) and gluten on the plasma metabolome in irritable bowel syndrome (IBS). They used SIRIUS and CSI:FingerID to annotate metabolites not available in spectral libraries. They found that FODMAPs changed the metabolome, impacting bile acids and beneficial metabolites. These correlated weakly with IBS symptoms. Gluten weakly affected lipids without clear IBS link. FODMAPs influenced health-positive metabolites despite minor symptom worsening, while gluten's impact was less relevant.

Keywords: CSI:FingerID, diseases, food, human