PubMed

Int J Biol Macromol. 2025 Jan 13:139863. doi: 10.1016/j.ijbiomac.2025.139863. Online ahead of print.ABSTRACTGanoderma lucidum is a traditional Chinese medicine used to treat Alzheimer's disease (AD), whose main active ingredient is polysaccharides. A heteropolysaccharide named GLPZ-1 was isolated from Ganoderma lucidum. GLPZ-1 (6.608 kDa) predominantly consisted of Glc and minor Gal. The results of GC-MS and NMR analyses indicated that the backbone of GLPZ-1 was mainly composed of 1,4-α-D-Glcp, 1,4,6-α-Glcp and a minor amount of 1,3,4-β-D-Glcp, which was substituted with complex side chains at C-6 of 1,4,6-α-D-Glcp and at C-3 of 1,3,4-β-D-Glcp. GLPZ-1 demonstrated a protective effect on AD rats by improving behavioral abnormalities, alleviating pathological damage and ameliorating levels of IL-6, IL-1β, TNF-α and Th17, which were associated with GLPZ-1 modulating the microbiota-gut-metabolomics of AD rats. GLPZ-1 regulated the gut microbiota in AD rats by increasing the abundance of Bacteroides, unclassified_Lachnospiraceae, Lactobacillus, Pediococcus, Oscillibacter, Lachnoclostridium and Bifidobacterium, while simultaneously reducing the abundance of Pseudomonas and Desulfovibrio. GLPZ-1 could regulate fecal metabolites in AD rats tending towards the normal levels. These regulated fecal metabolites belonged to fatty acid metabolism, cholesterol and bile acid metabolism, neurotransmitters and aromatic amino acid metabolism. These findings provide a preliminary research basis for the exploitation of GLPZ-1 as an effective drug to prevent and delay AD.PMID:39814286 | DOI:10.1016/j.ijbiomac.2025.139863

Gastroenterology. 2025 Jan 13:S0016-5085(25)00038-1. doi: 10.1053/j.gastro.2024.12.031. Online ahead of print.ABSTRACTBACKGROUND: To decipher the mechanisms underlying the protective role of the Mediterranean diet (MED) in Crohn's disease (CD), we explored the implications of adherence to MED on CD course, inflammatory markers, microbial and metabolite composition.METHODS: Patients with newly diagnosed CD were recruited and followed prospectively. MED adherence was assessed by repeated food frequency questionnaires (FFQ), using a predefined IBDMED score, alongside validated MED adherence screeners. Crohn's disease activity index (CDAI), C-reactive protein (CRP), fecal calprotectin and microbial composition (16S-rRNA-sequencing) were assessed each visit. Baseline serum and fecal samples were analyzed for targeted quantitative metabolomics.RESULTS: Consecutive patients: 271 (52% males, average age- 31±12 years, B1 phenotype- 75%). FFQ collected: 636 (range 1-5 FFQ per patient). Adherence to MED was associated with a non-complicated CD course, and inversely correlated with CDAI, fecal calprotectin, CRP and microbial dysbiosis index (all P < .05). Increasing adherence to MED over time correlated with reduced CDAI and inflammatory markers (P < .05). Adherence to MED correlated with a microbial cluster of commensals and short-chain fatty acid producers including Faecalibacterium, and with plant metabolites, vitamin derivatives and amino acids. Conversely, adherence to MED inversely correlated with a cluster of oral genera, Escherichia coli and Ruminococcus gnavus, known CD-associated species, and with tryptophan metabolites, ceramides and primary bile acids (FDR < .2).CONCLUSION: Adherence to MED is associated with beneficial clinical outcomes and decreased inflammatory markers. These may be driven by lower levels of primary bile-acids and microbial dysbiosis and a beneficial microbial and metabolite composition. Randomized controlled trials are needed to evaluate the role of MED in CD management.PMID:39814239 | DOI:10.1053/j.gastro.2024.12.031

Bioorg Med Chem Lett. 2025 Jan 13:130106. doi: 10.1016/j.bmcl.2025.130106. Online ahead of print.ABSTRACTHarmaline as a natural compound possessed a wide range of pharmacological activities. In this study, 22 novel harmaline-based derivatives were synthesized and screened for in vitro anti-proliferation activity against three cancer cell lines, HCT116, MCF7, and MGC803. The modification site was at the position N-9 of harmaline. The 24-hour IC50 of compound HL22 against HCT116, MGC803, and MCF7 was 3.84 ± 0.11 μM, 5.26 ± 0.46 μM, and 8.67 ± 0.13 μM, respectively. Compound HL22 significantly reduced the migratory ability of MGC803 cells. The monoclonal formation of MGC803 cells was also inhibited by HL22. The 1H NMR metabolomics analysis suggested that the antiproliferative mechanism could be associated for the metabolism of glycine, serine and threonine, the metabolism of taurine and hypotaurine, glutathione metabolism, and the metabolism of nicotinic acid and nicotinamide. The significance of this study is that the anti-cancer activity of the modified N-9 derivatives of harmaline has been explored for the first time.PMID:39814086 | DOI:10.1016/j.bmcl.2025.130106

Bioinformatics. 2025 Jan 15:btaf020. doi: 10.1093/bioinformatics/btaf020. Online ahead of print.ABSTRACTMOTIVATION: Microbiota-derived metabolites significantly impact host biology, prompting extensive research on metabolic shifts linked to the microbiota. Recent studies have explored both direct metabolite analyses and computational tools for inferring metabolic functions from microbial shotgun metagenome data. However, no existing tool specifically focuses on predicting changes in individual metabolite levels, as opposed to metabolic pathway activities, based on shotgun metagenome data. Understanding these changes is crucial for directly estimating the metabolic potential associated with microbial genomic content.RESULTS: We introduce PredCMB (Predicting Changes in Microbial metaBolites), a novel method designed to predict alterations in individual metabolites between conditions using shotgun metagenome data and enzymatic gene-metabolite networks. PredCMB evaluates differential enzymatic gene abundance between conditions and estimates its influence on metabolite changes. To validate this approach, we applied it to two publicly available datasets comprising paired shotgun metagenomics and metabolomics data from inflammatory bowel disease (IBD) cohorts and the cohort of gastrectomy for gastric cancer. Benchmark evaluations revealed that PredCMB outperformed a previous method by demonstrating higher correlations between predicted metabolite changes and experimentally measured changes. Notably, it identified metabolite classes exhibiting major alterations between conditions. By enabling the prediction of metabolite changes directly from shotgun metagenome data, PredCMB provides deeper insights into microbial metabolic dynamics than existing methods focused on pathway activity evaluation. Its potential applications include refining target metabolite selection in microbial metabolomic studies and assessing the contributions of microbial metabolites to disease pathogenesis.AVAILABILITY: Freely available to non-commercial users at https://www.sysbiolab.org/predcmb.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.PMID:39814067 | DOI:10.1093/bioinformatics/btaf020

Talanta. 2025 Jan 10;286:127566. doi: 10.1016/j.talanta.2025.127566. Online ahead of print.ABSTRACTMetabolites identification is the major bottleneck in untargeted LC-MS metabolomics, primarily due to the limited availability of MS2 information for most detected metabolites in data dependent acquisition (DDA) mode. To solve this problem, we have integrated the iterative, interval, and segmented window acquisition concepts to develop an innovative non-fixed segmented window interval data dependency acquisition (NFSWI-DDA) mode, which achieves comparable MS2 coverage to data independent acquisition (DIA) mode. This acquisition strategy harnesses the strengths of both DDA and DIA, which could provide extensive coverage and excellent reproducibility of MS2 spectra. Furthermore, utilizing the NFSWI-DDA data, we successfully acquired and identified a large-scale of multiple reaction monitoring (MRM) ion pairs, and transitioned them from high-resolution mass spectrometry (HRMS) to triple quadrupole mass spectrometry (TQ-MS). At last, a large-scale targeted metabolomics method was established practically. This method enables targeted analysis of 475 endogenous metabolites encompassing amino acids, nucleotides, bile acids, fatty acids, and carnitines, which could cover 9 major metabolic pathways as well as 65 secondary metabolic pathways. The established targeted method allows for semi-quantitative assessment of 475 metabolites while enabling quantitative analysis of 327 specific metabolites in biological samples. The method demonstrates immense potential in the detection of various biological samples, offering robust technical support and generating extensive data to advance applications in precision medicine and life sciences.PMID:39813915 | DOI:10.1016/j.talanta.2025.127566

Aquat Toxicol. 2025 Jan 14;279:107238. doi: 10.1016/j.aquatox.2025.107238. Online ahead of print.ABSTRACTAnticoccidials, commonly used in veterinary medicine to treat coccidiosis in food-producing animals, particularly in poultry farming, are associated with potential environmental risks due to their excretion in manure and subsequent land-spreading. Diclazuril, a widely used anticoccidial, has been detected in groundwater, raising concerns about its impact on non-target species. This study investigates the developmental toxicity of diclazuril in zebrafish embryos over a 96-hour exposure period, utilizing biomarkers such as oxidative stress indicators and metabolomic profiles. The acute toxicity assessment determined an LC50 of 255 µg/L for diclazuril. Observed sublethal effects included pericardial edema, curved spine, and yolk sac edema, which worsened with increasing concentrations from 106 µg/L to 515 µg/L. Based on the Lowest Observed Adverse Effect Level (LOAEL), further experiments were conducted at concentrations of 50 µg/L, 100 µg/L, and 200 µg/L. Significant increases in reactive oxygen species (ROS) were noted at 100 µg/L and 200 µg/L, alongside notable reduction in superoxide dismutase (SOD) and glutathione S-transferase (GST) activities at concentrations ≥100 µg/L, while no significant changes observed in catalase (CAT) activity. Metabolomic analysis using GC-MS/MS revealed significant disturbances in pathways such as pyruvate metabolism, the citric acid cycle, and amino acid metabolism, indicating potential mitochondrial dysfunction in groups exposed to concentrations ≥100 µg/L. Furthermore, alterations in histological lesions in brain region and altered neurotransmitter activity suggests possible neurobehavioral disorders. Increased oxidative stress, along with decreased ATP and NADH levels, points to mitochondrial dysfunction, which is further supported by ultrastructural analysis and locomotor behavior confirming mitochondrial disruption. The disruption of cellular energetics is likely a key factor contributing to the neurotoxic effects observed in zebrafish embryos exposed to ≥100 µg/L of diclazuril.PMID:39813883 | DOI:10.1016/j.aquatox.2025.107238

Food Chem. 2025 Jan 10;471:142844. doi: 10.1016/j.foodchem.2025.142844. Online ahead of print.ABSTRACTAvocado (Persea americana Mill) is a climacteric fruit harvested at the green stage that ripens postharvest to become edible. The 'Hass' cultivar, known for its rich, buttery flavor and pear-shaped appearance, was studied for metabolite changes during postharvest ripening using UPLC-MS/MS approach. The 16-day ripening period could be divided into three stages: evolution (days 1-9), edible ripe (days 10-15) and overripe (day 16). A total of 1397 metabolites were identified across 13 classes. Among them, amino acids transitioned from conjugated to free forms, while sugars converted to monosaccharides, enhancing savory and sweet tastes. The concentration of certain secondary metabolites like terpenes, coumarins, and alkaloids increased, likely supporting antimicrobial defense, alongside a substantial increase in lipid content. Additionally, 20 compounds were screened as markers for edible ripeness. This study provides valuable insights into avocado postharvest ripening and offers references for optimizing shelf-life.PMID:39813831 | DOI:10.1016/j.foodchem.2025.142844

Hepatol Commun. 2025 Jan 16;9(2):e0615. doi: 10.1097/HC9.0000000000000615. eCollection 2025 Feb 1.ABSTRACTBACKGROUND: Although bariatric and metabolic surgical methods, including duodenal-jejunal bypass (DJB), were shown to improve metabolic dysfunction-associated steatotic liver disease (MASLD) in clinical trials and experimental rodent models, their underlying mechanisms remain unclear. The present study therefore evaluated the therapeutic effects and mechanisms of action of DJB in rats with MASLD.METHODS: Rats with MASLD were randomly assigned to undergo DJB or sham surgery. Rats were orally administered a broad-spectrum antibiotic cocktail (Abx) or underwent fecal microbiota transplantation to assess the role of gut microbiota in DJB-induced improvement of MASLD. Gut microbiota were profiled by 16S rRNA gene sequencing and metagenomic sequencing, and bile acids (BAs) were analyzed by BA-targeted metabolomics.RESULTS: DJB alleviated hepatic steatosis and insulin resistance in rats with diet-induced MASLD. Abx depletion of bacteria abrogated the ameliorating effects of DJB on MASLD. Fecal microbiota transplantation from rats that underwent DJB improved MASLD in high-fat diet-fed recipients by reshaping the gut microbiota, especially by significantly reducing the abundance of Clostridium. This, in turn, suppressed secondary BA biosynthesis and activated the hepatic BA receptor, farnesoid X receptor. Inhibition of farnesoid X receptor attenuated the ameliorative effects of post-DJB microbiota on MASLD.CONCLUSIONS: DJB ameliorates MASLD by regulating gut microbiota and BA metabolism through hepatic farnesoid X receptor pathways.PMID:39813598 | DOI:10.1097/HC9.0000000000000615

PLoS One. 2025 Jan 15;20(1):e0315374. doi: 10.1371/journal.pone.0315374. eCollection 2025.ABSTRACTBehavioral dysfunctions in dogs represent one of the main social concerns, since they can endanger animals and human-dog relationship. Together with the trigger stimulus (human, animal, place, scent, auditory stimuli, objects), dogs can experience stressful conditions, either in multiple settings or unique situations, more often turning into generalized fear. Such a dysfunctional behavior can be associated with genetic susceptibility, environmental factors, traumatic experiences, and medical conditions. The available therapy, based on behavior approaches, environmental management, and neurochemical manipulation, through nutrition, supplements, medicines, and pheromones, represent the mainstays of the treatments currently accessible. Growing evidence in humans and animals highlight the importance of the gut-brain axis in the modulation of the brain physiology and behavior as well. Here, taking advantage of the next generation sequencing approach, we sought to investigate the potential connection between gut microbiota and microbiome in dogs suffering from generalized fear (n = 8), when compared to healthy subjects (n = 8), who all lived in different families. Faecal microbiota evaluation showed a differential abundance of taxa related to Proteobacteria and Firmicutes Phyla, between case and control dogs. Moreover, serum metabolomics documented significant alterations of molecules associated to GABA and glutamate neurotransmission in the patients, as well as bile acids metabolism. Overall, our preliminary and integrated investigations highlighted an intriguing role for the microbiome-metabolome network, allowing to further unveil the potential pathophysiology of relational issues in companion animals and paving the way for more effective therapeutical approaches.PMID:39813205 | DOI:10.1371/journal.pone.0315374

Mol Cell Biochem. 2025 Jan 15. doi: 10.1007/s11010-024-05198-4. Online ahead of print.ABSTRACTThe prognosis of B cell acute lymphoblastic leukemia (B-ALL) is poor, primarily due to drug resistance and relapse. Ga15, encoded by GNA15, belongs to the G protein family, with G protein-coupled receptors playing a crucial role in multiple biological process. GNA15 has been reported to be involved in various malignancies; however, its potential role in B-ALL remain unknown. In this study, high expression of GNA15 in B-ALL was observed in multiple databases. We further confirmed an increased transcriptional level of GNA15 in newly diagnosed B-ALL patients which was closely correlated with relapse. We showed that GNA15 promoted cell growth, inhibited apoptosis and enhanced drug resistance in leukemia cell lines. Metabolomics analysis revealed a significant enrichment of fatty acid oxidation (FAO) according to the GNA15 expression. We further confirmed that GNA15 could enhance FAO process as evidenced by the upregulation of key molecules involved in FAO including carnitine palmitoyl transferase1 (CPT1), CPT2 and CD36. And inhibition of FAO using etomoxir partially reversed the drug resistance caused by high expression of GNA15. Mechanism study showed that GNA15 promoted FAO by up-regulation of AMPK phosphorylation thus leading to survival advantage in leukemia cells. In conclusion, we observed elevated GNA15 transcript levels in B-ALL, which were associated with relapse. GNA15 could induce drug resistance though activation of the AMPK/FAO axis in leukemia cell lines. Targeting GNA15 and FAO may represent potential therapeutic strategy for improving the prognosis of B-ALL.PMID:39812998 | DOI:10.1007/s11010-024-05198-4

Methods Mol Biol. 2025;2891:269-276. doi: 10.1007/978-1-0716-4334-1_15.ABSTRACTMetabolomics is the area of research, which strives to obtain complete metabolic fingerprints, to detect differences between them and to provide hypothesis to explain those differences (Schripsema J, Dagnino D, Handbook of chemical and biological plant analytical methods. Wiley, New York, 2015). However, obtaining complete metabolic fingerprints is not an easy task. Metabolite extraction is a key step during this process, and much research has been devoted to finding the best solvent mixture to extract as much metabolites as possible.Here a procedure is described for analysis of both polar and apolar metabolites using a two-phase extraction system. D2O and CDCl3 are the solvents of choice, and their major advantage is that, for the identification of the compounds, standard databases can be used because D2O and CDCl3 are the solvents most commonly used for pure compound NMR spectra. The procedure enables the absolute quantification of components due to the addition of suitable internal standards. The extracts are also suitable for further analysis with other systems like LC-MS or GC-MS.PMID:39812988 | DOI:10.1007/978-1-0716-4334-1_15

Methods Mol Biol. 2025;2891:239-256. doi: 10.1007/978-1-0716-4334-1_13.ABSTRACTThe final aim of metabolomics is the comprehensive and holistic study of the metabolome in biological samples. Therefore, the use of instruments that enable the analysis of metabolites belonging to various chemical classes in a wide range of concentrations is essential, without compromising on robustness, resolution, sensitivity, specificity, and metabolite annotation. These characteristics are crucial for the analysis of very complex samples, such as wine, whose metabolome is the result of the sum of metabolites derived from grapes, yeast(s), bacteria(s), and chemical or physical modification during winemaking. In recent years, a big advantage, in this direction, was the hardware developments on hyphenated instruments that enable the integration of liquid chromatography (LC), ion mobility spectrometry (IMS), and mass spectrometry (MS). This chapter describes an LC-IMS-MS protocol for the analysis of wine and grape samples as well as the use of IMS data in metabolite annotation.PMID:39812986 | DOI:10.1007/978-1-0716-4334-1_13

Methods Mol Biol. 2025;2891:221-237. doi: 10.1007/978-1-0716-4334-1_12.ABSTRACTTrapped ion mobility spectrometry (TIMS) using parallel accumulation serial fragmentation (PASEF®) is an advanced analytical technique that offers several advantages in mass spectrometry (MS)-based lipidomics. TIMS provides an additional dimension of separation to mass spectrometry and accurate collision cross-section (CCS) measurements for ions, aiding in the structural characterization of molecules. This is especially valuable in lipidomics for identifying and distinguishing isomeric or structurally similar compounds. On the other hand, PASEF technology allows for fast and efficient data acquisition by accumulating ions in parallel and then serially fragmenting them. This accelerates the analysis process and improves throughput, making it suitable for high-throughput applications. Moreover, the combination of TIMS and PASEF reduces co-elution and ion coalescence issues, leading to cleaner and more interpretable mass spectra. This results in higher data quality and more confident identifications. In this chapter, a data-dependent TIMS-PASEF® workflow for lipidomics analysis is presented.PMID:39812985 | DOI:10.1007/978-1-0716-4334-1_12

Methods Mol Biol. 2025;2891:205-219. doi: 10.1007/978-1-0716-4334-1_11.ABSTRACTA simple analytical workflow is described for gas chromatographic-mass spectrometric (GC-MS)-based chiral profiling of secondary amino acids (AAs) in biological matrices. The sample preparation is carried out directly in aqueous biological sample extracts and involves in situ heptafluorobutyl chloroformate (HFBCF) derivatization-liquid-liquid microextraction of nonpolar products into hexane phase followed by subsequent formation of the corresponding methylamides from the HFB esters by direct treatment with methylamine reagent solution. The (O, N) HFB-butoxycarbonyl-methylamide AA products (HFBOC-MA) are separated on a Chirasil-L-Val capillary column and quantitatively measured by GC-MS operated in selected ion monitoring (SIM) mode. The protocol includes 12 simple pipetting steps and covers the quantitative analysis of 8 L, D pairs of secondary amino acids, including proline, isomeric 3-, 4-hydroxyprolines, pipecolic acid, nipecotic acid, azetidine-2-carboxylic acid, and cis- and trans-5-hydroxy-L-pipecolic acid using 13C5 -L-proline as an internal standard. The individual analytical steps are commented on and explained, with emphasis on the chiral GC-MS analysis of secondary amino acids in human urine, serum, and peptide hydrolysate samples.PMID:39812984 | DOI:10.1007/978-1-0716-4334-1_11

Methods Mol Biol. 2025;2891:181-204. doi: 10.1007/978-1-0716-4334-1_10.ABSTRACTMetabolomics aims at identification and quantitation of key end point metabolites, basically polar, in order to study changes in biochemical activities in response to pathophysiological stimuli or genetic modifications. Targeted profiling assays enjoying a growing popularity over the last years with LC-MS/MS as a powerful tool for development of such (semi-)quantitative methods for a large number of metabolites. Here we describe a method for absolute quantitation of ca. 100 metabolites belonging to key metabolite classes such as sugars, amino acids, nucleotides, organic acids, and amines with a hydrophilic interaction liquid chromatography (HILIC) system comprised with ultra (high) performance liquid chromatography (UHPLC) with detection on a triple quadrupole mass spectrometer operating in both positive and negative modes.PMID:39812983 | DOI:10.1007/978-1-0716-4334-1_10

Methods Mol Biol. 2025;2891:165-180. doi: 10.1007/978-1-0716-4334-1_9.ABSTRACTA protocol for the preparation of tissue extracts for the targeted analysis ca. 150 polar metabolites, including those involved in central carbon metabolism, is described, using a reversed phase ion pair U(H)PLC-MS method. Data collection enabled in high-resolution mass spectrometry detection provides highly specific and sensitive acquisition of metabolic intermediates with wide range physicochemical properties and pathway coverage. Technical aspects are discussed for method transfer along with the basic principles of sample sequence setup, data analysis, and validation. At last general comments are given to help the assessment of data quality and system performance.PMID:39812982 | DOI:10.1007/978-1-0716-4334-1_9

Methods Mol Biol. 2025;2891:153-163. doi: 10.1007/978-1-0716-4334-1_8.ABSTRACTThe gut's symbiome, a hidden metabolic organ, has gained scientific interest for its crucial role in human health. Acting as a biochemical factory, the gut microbiome produces numerous small molecules that significantly impact host metabolism. Metabolic profiling facilitates the exploration of its influence on human health and disease through the symbiotic relationship. Fecal metabolomics-based analysis is an indisputably valuable tool for elucidating the biochemistry of digestion and absorption in the gastrointestinal system, serving as the most suitable specimen to study the symbiotic relationship between the host and the intestinal microbiota. It is well-established that the balance of the intestinal microbiota changes in response to various stimuli, both physiological, such as gender, age, diet, and exercise, and pathological, such as gastrointestinal and hepatic diseases. Fecal samples have been analyzed using widely adopted analytical techniques, including NMR spectroscopy, GC-MS, and LC-MS/MS. Rat fecal samples are frequently used and particularly useful substrates for metabolomics-based studies in related fields.The complexity and diversity of fecal samples necessitate careful and skillful handling to extract metabolites, while avoiding their deterioration, effectively and quantitatively. Several determinative factors, such as the fecal sample weight to extraction solvent solution volume, the nature and pH value of the extraction solvent, and the homogenization process, play crucial roles in achieving optimal extraction for obtaining high-quality metabolic fingerprints, whether for untargeted or targeted metabolomics.PMID:39812981 | DOI:10.1007/978-1-0716-4334-1_8

Methods Mol Biol. 2025;2891:131-152. doi: 10.1007/978-1-0716-4334-1_7.ABSTRACTLipidomics has attracted attention in the discovery of unknown biomolecules and for capturing the changes in metabolism caused by genetic and environmental factors in an unbiased manner. However, obtaining reliable lipidomics data, including structural diversity and quantification data, is still challenging. Supercritical fluid chromatography (SFC) is a suitable technique for separating lipid molecules with high throughput and separation efficiency. Here, we describe a quantitative lipidomics method using SFC coupled with mass spectrometry. This technique is suitable for characterizing the structural diversity of lipids (e.g., phospholipids, sphingolipids, glycolipids, and glycerolipids) with high quantitative accuracy to understand their biological functions.PMID:39812980 | DOI:10.1007/978-1-0716-4334-1_7

Methods Mol Biol. 2025;2891:109-129. doi: 10.1007/978-1-0716-4334-1_6.ABSTRACTUntargeted analysis by LC-MS is a valuable tool for metabolic profiling (metabonomics/metabolomics), and applications of this technology have grown rapidly over the past decade. LC-MS offers advantages of speed, sensitivity, relative ease of sample preparation, and large dynamic range compared to other platforms in this role. However, like any analytical approach, there are still drawbacks and challenges that have to be overcome, some of which are being addressed by advances in both column chemistries and instrumentation. In particular, the combination of LC-MS with ion mobility offers many new possibilities for improved analyte separation, detection, and structural identification. There are many untargeted LC-MS approaches which can be applied to metabolic phenotyping, and these usually need to be optimized for the type of sample, the nature of the study, or the biological question. Some of the main LC-MS approaches for untargeted metabolic phenotyping are described in detail in the following protocol.PMID:39812979 | DOI:10.1007/978-1-0716-4334-1_6

Methods Mol Biol. 2025;2891:91-108. doi: 10.1007/978-1-0716-4334-1_5.ABSTRACTLiquid Chromatography-Mass Spectrometry (LC-MS) untargeted experiments require complex bioinformatic strategies to extract information from the experimental data. Here we discuss the "data preprocessing," the set of procedures performed on the raw data to produce a data matrix which will be the starting point for the subsequent statistical analysis. Data preprocessing is a crucial step on the path to knowledge extraction, which should be carefully controlled and optimized in order to maximize the output of any untargeted metabolomics investigation.PMID:39812978 | DOI:10.1007/978-1-0716-4334-1_5