LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Assessment of automated trimethylsilyl derivatisation protocols for GC-MS-based untargeted metabolomic analysis of urine'.
Answer: GC-MS is a commonly used metabolomic platform for the analysis of urine. A key step in the preparation of samples for GC-MS is derivatisation, in particular, methoximation and trimethylsilylation. This paper presents an assessment of automated derivatisation protocols for GC-MS-based untargeted metabolomic analysis of rat urine. Automated batch and in-time (a sample ready for injection every 70 minutes) derivatisation protocols were tested using BSTFA and MSTFA. Principal component analysis determined differences based upon protocol tested (PC-1; 19%) and silylation reagent (PC-2; 17%) used. Of 249 compounds, 40 compounds were significantly different (P<0.05) based upon reagent and 154 compounds were significantly different (P<0.05) based upon protocol. A key outcome of this study was the demonstrated effects of derivatisation including reagent and protocol (i.e. reaction duration, temperature and mixing speed) on individual urinary metabolites. It is hoped that the current work will provide a reference on which to base future GC-MS-based untargeted and targeted metabolomic analyses of urine.
Question: Write a study description for the study titled 'Metabolic fingerprinting reveals a novel candidate biomarker for prednisolone treatment in cattle'.
Answer: The use of glucocorticoids as growth promoters for meat-producing animals is strictly regulated within the European Union. However, in the past few years, a higher frequency of non-compliant bovine urine samples for prednisolone has been noticed, which could not be directly related to fraudulent use of prednisolone. As such, questions have risen about the origin of this compound. Unfortunately, at present, no decisive strategy has been established to discriminate between endogenous and exogenous prednisolone. In this study, an untargeted metabolomics strategy, based on Orbitrap and QqTOF mass spectrometry, was deployed to reveal urinary biomarkers, which are indicative for the exogenous administration of the synthetic glucocorticoid prednisolone. For this purpose, prednisolone was administered intramuscularly and per os to 12 bovines and a total of 2700 urine samples were collected before, during and after treatment. Multivariate statistical data analysis (i.e. OPLS-DA) revealed four differentiating metabolites that allowed discrimination between urine samples collected before and during prednisolone administration. None of these compounds were present in urine containing endogenous prednisolone, of which the formation was induced by the administration of a synthetic analogue of adrenocorticotropic hormone. Only one metabolite was retained as a highly suitable biomarker during growth-promoting and therapeutic prednisolone treatment, with 93.4 % sensitivity and 96.3 % specificity. Besides, this compound could be detected up to 4 days after a single therapeutic per os prednisolone administration. Based on accurate mass, isotope pattern, and MS/MS spectra, this compound was putatively annotated and is suggested as an actionable biomarker for exogenous prednisolone administration.
Question: Write a study description for the study titled 'Altered fecal microbial and metabolic profiles reveal potential mechanisms underlying anemia in patients with chronic renal failure'.
Answer: The gut microbiomes communicate with kidney and may play a crucial role in the development of anemia in patients with chronic renal failure (CRF). However, the alterations in microbiota and their association with functional metabolites remain unclear. We performed metagenomics and untargeted metabolomics in a cohort of 30 patients with anemia of CRF and 20 healthy controls (HCs) to identify the characteristics of the gut microbiome and explore its potential interactions with the host. Decreased microbiota diversity and significant compositional differences were observed in the patients with anemia of CRF. We identified six gut microbiotas significantly changed in patients with anemia of CRF, particularly Faecalibacterium prausnitzii, Prevotella copri and Escherichia coli that were closely correlated with hemoglobin (Hb) levels and estimated glomerular filtration rate. And these changes were accompanied by functional alterations in distinctive microbial pathways. Further fecal and serum metabolomics revealed fecal 12-KETE-LB4 in arachidonic acid metabolism, uracil and L-aspartic acid in beta-alanine metabolism, gulonic acid in ascorbate and aldarate metabolism, accompanied by the top 15 differential serum metabolites were closely correlated with Hb levels. Furthermore, we observed a complex co-occurrence between anemia of CRF-related gut microbiota species and the characterized metabolites. Moreover, a non-invasive model incorporating Faecalibacterium prausnitzii, Prevotella copri, combined with fecal 12-KETE-LB4, uracil, L-aspartic acid and gulonic acid, distinguished patients with anemia of CRF from HCs (area under the curve: 0.879). Collectively, our results suggest that a disordered gut microbiome associated with functional metabolites may be a non-invasive diagnostic and therapeutic target for anemia of CRF.Linked studies: UPLC-MS assays of Fecal samples are reported in this study.UPLC-MS assays of Blood Plasma samples are reported in MTBLS12576.
Question: Write a study description for the study titled 'Phosphoproteomic and Metabolomic Profiling Uncovers the Roles of CcPmk1 in the Pathogenicity of Cytospora chrysosperma'.
Answer: Pmk1, a highly conserved pathogenicity-related mitogen-activated protein kinase (MAPK) in pathogenic fungi, is phosphorylated and activated by MAP2K and acts as a global regulator of fungal infection and invasive growth by modulating downstream targets. However, the hierarchical CcPmk1 regulatory network in Cytospora chrysosperma, the main causal agent of canker disease in many woody plant species, is still unclear. In this study, we analyzed and compared the phosphoproteomes and metabolomes of ΔCcPmk1 and wild-type strains and identified pathogenicity-related downstream targets of CcPmk1. We found that CcPmk1 could interact with the downstream homeobox transcription factor CcSte12 and affect its phosphorylation. In addition, the ΔCcSte12 displayed defective phenotypes that were similar to yet not identical to that of the ΔCcPmk1 and included significantly reduced fungal growth, conidiation and virulence. Remarkably, CcPmk1 could phosphorylate proteins translated from a putative secondary metabolism-related gene cluster, which is specific to C. chrysosperma, and the phosphorylation of several peptides was completely abolished in the ΔCcPmk1. Functional analysis of the core gene (CcPpns1) in this gene cluster revealed its essential roles in fungal growth and virulence. Metabolomic analysis showed that amino acid metabolism and biosynthesis of secondary metabolites, lipids, and lipid-like molecules significantly differed between wild type and ΔCcPmk1. Importantly, most of the annotated lipids and lipid-like molecules were significantly downregulated in the ΔCcPmk1 compared to the wild type. Collectively, these findings suggest that CcPmk1 may regulate a small number of downstream master regulators to control fungal growth, conidiation and virulence in C. chrysosperma.Data availability:The proteomics data have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD032206.
Question: Write a study description for the study titled 'Integrated gut metabolome and microbiome fingerprinting reveals that dysbiosis precedes allergic inflammation in IgE‐mediated pediatric cow's milk allergy'.
Answer: BACKGROUND: IgE-mediated cow's milk allergy (IgE-CMA) is one of the first allergies to arise in early childhood and may result from exposure to various milk allergens, of which β-lactoglobulin (BLG) and casein are the most important. Understanding the underlying mechanisms behind IgE-CMA is imperative for the discovery of novel biomarkers and the design of innovative treatment and prevention strategies.METHODS: We report a longitudinal in vivo murine model, in which two mice strains (BALB/c and C57Bl/6) were sensitized to BLG using either cholera toxin or an oil emulsion (n = 6 per group). After sensitization, mice were challenged orally, their clinical signs monitored, antibody (IgE and IgG1) and cytokine levels (IL-4 and IFN-γ) measured, and fecal samples subjected to metabolomics. The results of the murine models were further extrapolated to fecal microbiome-metabolome data from our population of IgE-CMA (n = 22) and healthy (n = 23) children (Trial: NCT04249973), on which polar metabolomics, lipidomics and 16S rRNA metasequencing were performed. In vitro gastrointestinal digestions and multi-omics corroborated the microbial origin of proposed metabolic changes.RESULTS: During mice sensitization, we observed multiple microbially derived metabolic alterations, most importantly bile acid, energy and tryptophan metabolites, that preceded allergic inflammation. We confirmed microbial dysbiosis, and its associated effect on metabolic alterations in our patient cohort, through in vitro digestions and multi-omics, which was accompanied by metabolic signatures of low-grade inflammation.CONCLUSION: Our results indicate that gut dysbiosis precedes allergic inflammation and nurtures a chronic low-grade inflammation in children on elimination diets, opening important new opportunities for future prevention and treatment strategies.
Question: Write a study description for the study titled 'Deciphering the metabolic perturbation in hepatic alveolar echinococcosis: a 1H NMR-based metabolomics study'.
Answer: BACKGROUND: Hepatic alveolar echinococcosis (HAE) is caused by the growth of Echinococcus multilocularis larvae in the liver. It is a chronic and potentially lethal parasitic disease. Early stage diagnosis for this disease is currently not available due to its long asymptomatic incubation period. In this study, a proton nuclear magnetic resonance (1H NMR)-based metabolomics approach was applied in conjunction with multivariate statistical analysis to investigate the altered metabolic profiles in blood serum and urine samples obtained from HAE patients. The aim of the study was to identify the metabolic signatures associated with HAE.RESULTS: A total of 21 distinct metabolic differences between HAE patients and healthy individuals were identified, and they are associated with perturbations in amino acid metabolism, energy metabolism, glyoxylate and dicarboxylate metabolism. Furthermore, the present results showed that the Fischer ratio, which is the molar ratio of branched-chain amino acids to aromatic amino acids, was significantly lower (P < 0.001) in the blood serum obtained from the HAE patients than it was in the healthy patient group.CONCLUSIONS: The altered Fischer ratio, together with perturbations in metabolic pathways identified in the present study, may provide new insights into the mechanistic understanding of HAE pathogenesis and potential therapeutic interventions.
Question: Write a study description for the study titled 'Sex Differences in Colon Cancer Metabolism Reveal A Novel Subphenotype (UPLC-MS RP POS assay)'.
Answer: Women have a lower incidence of colorectal cancer (CRC) than men, however, they have a higher incidence of right-sided colon cancer (RCC). This is of concern as patients with RCC have the poorest clinical outcomes among all CRC patients. Aberrant metabolism is a known hallmark and therapeutic target for cancer. We propose that metabolic subphenotypes exist between CRCs due to intertumoral molecular and genomic variation, and differences in environmental milieu of the colon which vary between the sexes. Metabolomics analysis of patient colon tumors (n = 197) and normal tissues (n = 39) revealed sex-specific metabolic subphenotypes dependent on anatomic location. Tumors from women with RCC were nutrient-deplete, showing enhanced energy production to fuel asparagine synthesis and amino acid uptake. The clinical importance of our findings were further investigated in an independent data set from The Cancer Genomic Atlas, and demonstrated that high asparagine synthetase (ASNS) expression correlated with poorer survival for women. This is the first study to show a unique, nutrient-deplete metabolic subphenotype in women with RCC, with implications for tumor progression and outcomes in CRC patients.UPLC-MS HILIC POS assay is reported in MTBLS1122.UPLC-MS HILIC NEG assay is reported in MTBLS1124.UPLC-MS RP POS assay is reported in MTBLS1129.UPLC-MS RP NEG assay is reported in MTBLS1130.
Question: Write a study description for the study titled 'Gut microecology of long COVID persisting for 2 years'.
Answer: Long COVID is an emerging global public health issue. The human gut microbiota (GM) has been identified as a potentially important factor influencing the development of long COVID. This study aims to understand the prevalence, risk factors and GM of long COVID persisting for 2 years in Hainan Province, China, to aid public recognition.
Question: Write a study description for the study titled 'Multi-omics analysis reveals the mechanism of Lacticaseibacillus paracasei IMAUJBC1 in alleviating hyperlipidemia'.
Answer: This study investigated the alleviating effect of Lacticaseibacillus paracasei IMAUJBC1 on hyperlipidemia and explored the associated mechanism by combining microbiome, transcriptomic and lipomic analyses. The high-fat mouse model was established with a high-fat diet (HFD), and the intervention of IMAUJBC1 was conducted for 8 weeks after modeling. The results showed that IMAUJBC1 inhibited weight gain and liver fat accumulation in HFD mice, reduced total cholesterol (T-CHO) and low-density lipoprotein cholesterol (LDL-C) serum levels, promoted the conversion of liver cholesterol to total bile acid (TBA), and increased fecal T-CHO excretion. The IMAUJBC1 intervention decreased the ratio of Firmicutes and Bacteroidetes, while the abundance of Alistipes was increased in mice gut microbiome. IMAUJBC1 may alleviate hyperlipidemia through the PPAR signaling pathway, fat digestion and absorption, cholesterol metabolism, and glycerophospholipid metabolism. In summary, IMAUJBC1 can be used as a functional lactobacillus to intervene in hyperlipidemia.
Question: Write a study description for the study titled 'Metabolomic assessment of acute cholestatic injuries induced by thioacetamide and by bile duct ligation, and the protective effects of Huang-Lian-Jie-Du-Decoction'.
Answer: Huang-Lian-Jie-Du-Decoction, a traditional Chinese formula, has been reported to protect liver from various injuries. Two cholestasis models of rats induced by thioacetamide and by bile duct ligation were established and treated with Huang-Lian-Jie-Du-Decoction. Nuclear Magnetic Resonance-based urinary metabolic profiles were analyzed by orthogonal partial least squares discriminant analysis and univariate analysis to excavate differential metabolites associated with the injuries of the two models and the treatment effects of Huang-Lian-Jie-Du-Decoction. The two cholestatic models shared common metabolic features of excessive fatty acid oxidation, insufficient glutathione regeneration and disturbed gut flora, with specific characteristics of inhibited urea cycle and DNA damage in thioacetamide-intoxicated model, and perturbed Kreb's cycle and inhibited branched chain amino acid oxidation in bile duct ligation model. With good treatment effects, Huang-Lian-Jie-Du-Decoction could regain the balance of the disturbed metabolic status common in the two cholestasis injuries, e.g., unbalanced redox system and disturbed gut flora; and perturbed urea cycle in thioacetamide-intoxicated model and energy crisis (disturbed Kreb's cycle and oxidation of branched chain amino acid) in bile duct ligation model, respectively.
Question: Write a study description for the study titled 'Elevated brain manganese induces motor disease by upregulating the kynurenine pathway of tryptophan metabolism'.
Answer: Elevated brain levels of the essential metals manganese (Mn), copper, or iron induce motor disease. However, mechanisms of metal-induced motor disease are unclear and treatments are lacking. Elucidating the mechanisms of Mn-induced motor disease is particularly important because occupational and environmental Mn overexposure is a global public health problem. To address this, here we combined unbiased transcriptomics and metabolomics with functional studies in a mouse model of human environmental Mn exposure. Transcriptomics unexpectedly revealed that Mn exposure up-regulated expression of metabolic pathways in the brain and liver. Notably, genes in the kynurenine pathway of tryptophan metabolism, which produces neuroactive metabolites that impact neurological function, were up-regulated by Mn. Subsequent unbiased metabolomics revealed that Mn treatment altered kynurenine pathway metabolites in the brain and liver. Functional experiments then demonstrated that pharmacological inhibition of the first and rate-limiting step of the kynurenine pathway fully rescued Mn-induced motor deficits. Finally, elevated Mn directly activates hypoxia-inducible factor (HIF) transcription factors, and additional mechanistic assays identified a role for HIF1, but not HIF2, in regulating expression of hepatic kynurenine pathway genes under physiological or Mn exposure conditions, suggesting that Mn-induced HIF1 activation may contribute to the dysregulation of the kynurenine pathway in Mn toxicity. These findings (1) identify the upregulation of the kynurenine pathway by elevated Mn as a fundamental mechanism of Mn-induced motor deficits; (2) provide a pharmacological approach to treat Mn-induced motor disease; and (3) should broadly advance understanding of the general principles underlying neuromotor deficits caused by metal toxicity.
Question: Write a study description for the study titled 'Isotopomer analysis of MCF-7 breast cancer cell line incubated with 13C labelled glucose (GC-MS assay)'.
Answer: MS and NMR are two of the most powerful spectroscopic techniques used in the field of fluxomics, to analyze the flux distributions in cellular metabolomic pathways. Both of them possess pros and cons, such as, MS being the most sensitive and low-cost technique, while needs extensive sample processing and providing incomplete labeling data, whereas NMR needs lesser sample preparation and provides more detailed labeling data, while being less sensitive and expensive. Since both techniques could be viewed as complementary to each other, combining their data could yield a detailed and complete information about a system under study. In this case, samples were generated from a single experiment and the same set of samples was used both in MS and 1D NMR to analyze the 13C label distributions in TCA cycle intermediates. The data generated from both methods were used with a simulation script that was developed to integrate the MS and NMR data. MCF-7 breast cancer cell line was used as an experimental model and it was incubated with 100% [1,2-13C]-glucose and 100% [U-13C]-glucose for 8 hours. The cells, before and after incubation with tracers, were frozen in liquid nitrogen and then later processed for extracting the TCA cycle intermediates. Same set of samples were separated for GC-MS and NMR based analysis and processed for the respective techniques. The isotopologue analysis was performed by GC-MS and the isotopomer analysis was performed by NMR and both sets of data were integrated with the simulation software. This study contains the data for GC-MS analysis.  The NMR assay for this study can be found in the MetaboLights study MTBLS241. Linked Studies: MTBLS241
Question: Write a study description for the study titled 'Comparison of Full-Scan, Data-Dependent, and Data-Independent Acquisition Modes in Liquid Chromatography-Mass Spectrometry Based Untargeted Metabolomics'.
Answer: Full-scan, data-dependent acquisition (DDA), and data-independent acquisition (DIA) are the three common data acquisition modes in high resolution mass spectrometry-based untargeted metabolomics. It is an important yet underrated research topic on which acquisition mode is more suitable for a given untargeted metabolomics application. In this work, we compared the three data acquisition techniques using a standard mixture of 134 endogenous metabolites and a human urine sample. Both hydrophilic interaction and reversed-phase liquid chromatographic separation along with positive and negative ionization modes were tested. Both the standard mixture and urine samples generated consistent results. Full-scan mode is able to capture the largest number of metabolic features, followed by DIA and DDA (53.7% and 64.8% respective features fewer on average in urine than full-scan). Comparing the MS2 spectra in DIA and DDA, spectra quality is higher in DDA with average dot product score 83.1% higher than DIA in Urine(H), and the number of MS2 spectra (spectra quantity) is larger in DIA (on average 97.8% more than DDA in urine). Moreover, a comparison of relative standard deviation distribution between modes shows consistency in the quantitative precision, with the exception of DDA showing a minor disadvantage (on average 19.8% and 26.8% fewer features in urine with RSD < 5% than full-scan and DIA). In terms of data preprocessing convenience, full-scan and DDA data can be processed by well-established software. In contrast, several bioinformatic issues remain to be addressed in processing DIA data and the development of more effective computational programs is highly demanded.
Question: Write a study description for the study titled 'Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry'.
Answer: Three-dimensional imaging mass spectrometry (3D imaging MS) is a technique of analytical chemistry for 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Due to the sheer quantity of data generated, visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed for evaluation and comparison of algorithms. Findings We acquired high-quality 3D imaging MS datasets from different biological systems at several labs, supplied them with overview images and scripts demonstrating how to read them, and deposited them into MetaboLights, an open repository for metabolomics data. 3D imaging MS data was collected from five samples using two types of 3D imaging MS. 3D Matrix-Assisted Laser Desorption/Ionization (MALDI) imaging MS data was collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D Desorption Electrospray Ionization (DESI) imaging MS data was collected from a human colorectal adenocarcinoma. Conclusions With the aim to stimulate computational research in the field of computational 3D imaging MS, we provided selected high-quality 3D imaging MS datasets which can be used by algorithm developers as benchmark datasets.