LC-MS-based multi-omics analysis of brain tissue for the evaluation of the anti-ischemic stroke potential of Tribulus terrestris L. fruit extract in MCAO rats

This study aimed to investigate the chemical composition of Tribulus terrestris L. fruit (TT) extract named TT15 and its protective effect against ischemic stroke (IS) as well as corresponding mechanisms. The chemical composition of TT15 was analyzed by liquid chromatography-mass spectrometry (LC-MS), and the compound identification was conducted via searching the in-house database. The LC-MS-based multi-omics approach was applied to search the differential metabolites and differential proteins in rat brain tissue and to explore the biomarker and molecular mechanism of TT15 against middle cerebral artery occlusion (MCAO). A total of 20 compounds were identified from TT15, mainly including alkaloids, flavonoids, phenols, quinones, and esters. These 20 compounds significantly affected the metabolism of 44 metabolites and the expression of 51 proteins. Joint pathway analysis showed that these metabolites and proteins were mainly involved in the response to elevated platelet cytosolic Ca²⁺ and platelet activation, which inferred that TT15 may exert a protective effect against cerebral ischemic injury via regulating platelet function. This study provides useful information for further exploration of the mechanisms of TT extract against IS.     

Metabolomics techniques applied in the investigation of phenolic acids from the agro-industrial by-product of Carapa guianensis Aubl

Processing of Carapa guianensis seeds to obtain oil on an industrial scale generates a significant amount of by-product, approximately 66% w/w, which is called cake and is a potential source of biomolecules, including simple phenolic structures. For this reason, studies were carried out on the chemical profiles of hydrolyzed extract from this agro-industrial by-product through High Performance Thin-Layer Chromatography (HPTLC) and Gas Chromatography coupled to Mass Spectrometry (GC–MS). These techniques were used to detect metabolic classes and/or groups, and to identify, for the first time, thirteen simple phenolic acids in this by-product. The sample antioxidant capacity was determined by methods of 2,2-diphenyl-1-picrylhydrazyl (DPPH)and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS⁺) radicals direct sequestration. The hydrolyzed fraction showed a total of 63.47% in the relative abundance of the total of compounds, standing out: p-hydroxybenzoic acid (39.19%) and protocatechuic acid (3,4-dihydroxybenzoic acid) (5.62%), both from hydroxybenzoic acids and 3-(3,4-dihydroxyphenyl)lactic acid, (7.76%) hydroxycinnamic acids derivatives. In these results, the fraction rich in simple phenolic acids was obtained, attributing the prominent behavior of this matrix antioxidant activity, expressed by (IC₅₀: of 16.42 µg/mL and 6.52 µg/mL for DPPH and ABTS⁺ radicals, respectively). The research demonstrated an alternative to applicability that involves sustainability from agro-industrial. These techniques were used to detect metabolic classes and/or groups, and to identify, for the first time, thirteen simple phenolic acids in this by-product, generating a process capable of converting biomass into a bioproduct, consisting of bioactive compounds, in addition to adding value to the industrial chain.     

Metabolites identification of oil palm roots infected with Ganoderma boninense using GC–MS-based metabolomics

An approach to metabolomics profiling of non-infected and Ganoderma boninense (G. boninsense) infected oil palm roots crude extracts that utilize gas chromatography-mass spectrometry (GC–MS) and multivariate statistics of principal component analysis (PCA) have been tested. This combination has provided a rapid approach in investigating the changes in the metabolite variations of non-infected and infected oil palm roots at 14 and 30 days post-infection. The extracts were prepared by using 80% (v/v) of methanol. In identifying the metabolites responsible for each differentiation, PCA model was generated in loading bi-plot. Dimethyl benzene-1,4-dicarboxylate, methyl 3-(3,5-ditert-butyl-4-hydroxyphenyl)propanoate, ergost-5-en-3-ol, (3β), stigmast-5-en-3-ol, (3β), stigmasterol, methyl hexadecanoate, methyl (9Z,12Z)-octadeca-9,12-dienoate, methyl octadecanoate, 2-(hydroxymethyl)-2-nitropropane-1,3-diol, methyl (Z)-octadec-6-enoate and (E)-icos-5-ene were found more abundant in G. boninense infected roots than in non-infected roots. Steroidal compounds and fatty acid derivatives which has been determined in the non-infected and G. boninense infected roots regulate a variety of responses to the G. boninense. The abundant of these metabolites in G. boninense infected roots are due to the crucial roles in pathogen defence.     

Metabolic mapping of Schisandra sphenanthera extract and its active lignans using a metabolomic approach based on ultra high performance liquid chromatography with high‐resolution mass spectrometry

Schisandra sphenanthera , the dried ripe fruit of Schisandra sphenanthera Rehd. et Wils , is widely used as a restorative, tonic and nutrition in many countries. Wuzhi tablet, an ethanol extract preparation of Schisandra sphenanthera , is a well‐known herbal medicine widely used in China. Our previous studies show that Wuzhi tablet and its active lignans significantly protect liver injury. However, its metabolic profile remains unknown in vivo and in vitro . In this study, ultra high performance liquid chromatography coupled with electrospray ionization high‐resolution mass spectrometry based metabolomics was employed to decipher the metabolic map of Wuzhi tablet and its active lignans. Serum (2 h) and urine (24 h) samples after a 700 mg/kg single oral dose of Wuzhi tablet, and mice liver microsome samples after incubation with its active lignans were collected and analyzed. The data were further analyzed using metabolomics and metabolite identification software. In total, 33 metabolites in vivo and 34 metabolites in vitro were identified, and six among them were new metabolites. The major metabolic reactions encompassed demethylation, hydroxylation, dehydrogenation, and epoxidation. Taken together, in vitro and in vivo studies revealed the metabolic profile of Wuzhi tablet and its active lignans and demethylation and hydroxylation were their major metabolic pathways.     

Evaluation of ion mobility in capillary electrophoresis coupled to mass spectrometry for the identification in metabolomics

Currently, feature annotation remains one of the main challenges in untargeted metabolomics. In this context, the information provided by high-resolution mass spectrometry (HRMS) in addition to accurate mass can improve the quality of metabolite annotation, and MS/MS fragmentation patterns are widely used. Accurate mass and a separation index, such as retention time or effective mobility (μ_eff), in chromatographic and electrophoretic approaches, respectively, must be used for unequivocal metabolite identification. The possibility of measuring collision cross-section (CCS) values by using ion mobility (IM) is becoming increasingly popular in metabolomic studies thanks to the new generation of IM mass spectrometers. Based on their similar separation mechanisms involving electric field and the size of the compounds, the complementarity of ^DTCCS_N2 and μ_eff needs to be evaluated. In this study, a comparison of ^DTCCS_N2 and μ_eff was achieved in the context of feature identification ability in untargeted metabolomics by capillary zone electrophoresis (CZE) coupled with HRMS. This study confirms the high correlation of ^DTCCS_N2 with the mass of the studied metabolites as well as the orthogonality between accurate mass and μ_eff, making this combination particularly interesting for the identification of several endogenous metabolites. The use of IM-MS remains of great interest for facilitating the annotation of neutral metabolites present in the electroosmotic flow (EOF) that are poorly or not separated by CZE.     

Phenylmethanesulfonyl fluoride pretreatment stabilizes plasma lipidome in lipidomic and metabolomic analysis

Though it is standard practice to test the stability of analytes in the matrix for routine bioanalytical method, stability evaluation is always impractical and skipped in untargeted lipidomic and metabolomic analysis because analytes in these studies are enormous, diverse and sometimes unknown. Lipidome represents a major class of plasma metabolome and shows great potential to be diagnostic and prognostic biomarkers. However, lipidome also faces stability problems because plasma contains kinds of lipid degradation enzyme. Here, using liquid chromatography time of flight mass spectrometry based lipidomic methodology, plasma levels of various lipids including triglyceride (TG), diglyceride (DG), free fatty acid (FFA), phosphatidylethanolamine (PE) phosphatidylcholine (PC), lyso-phosphatidylcholine (LPC), lyso-phosphatidylethanolamine (LPE), and sphingomyelin (SM) were dynamically determined within 4 h at ambient temperature. In mouse and rat plasma, the levels of most TG, DG, PC and PE species significantly decreased with respect to time, whereas those of LPC, LPE and FFA significantly increased with respect to time. However, such changes did not occur in human plasma, thus indicating hepatic lipase and esterase might involve in the species-specified degradation of lipid classes in plasma. Phenylmethanesulfonyl fluoride (PMSF) pretreatment prevented such lipidome instability in mouse plasma. The results suggested the instability of plasma lipidome should be highly concerned, and the enhancement of ex vivo stability of plasma lipidome could enable more reliable clinical translation of lipidomic data for biomarker discovery.     

Missing value imputation strategies for metabolomics data

The origin of missing values can be caused by different reasons and depending on these origins missing values should be considered differently and dealt with in different ways. In this research, four methods of imputation have been compared with respect to revealing their effects on the normality and variance of data, on statistical significance and on the approximation of a suitable threshold to accept missing data as truly missing. Additionally, the effects of different strategies for controlling familywise error rate or false discovery and how they work with the different strategies for missing value imputation have been evaluated. Missing values were found to affect normality and variance of data and k‐means nearest neighbour imputation was the best method tested for restoring this. Bonferroni correction was the best method for maximizing true positives and minimizing false positives and it was observed that as low as 40% missing data could be truly missing. The range between 40 and 70% missing values was defined as a “gray area” and therefore a strategy has been proposed that provides a balance between the optimal imputation strategy that was k‐means nearest neighbor and the best approximation of positioning real zeros.     

Identification of the new chymotrypsin inhibitor micropeptin 996 by metabolomics-guided analysis

An untargeted metabolomics approach was used to investigate a cultured strain of Microcystis aeruginosa (UTEX LB2386) known to be a prolific producer of a diverse class of cyanopeptides. Identification of a putative new compound with a molecular weight of 996 led to the purification and structure elucidation of this new member of the micropeptin class of cyanopeptides. Micropeptin 996 displayed potent inhibition of the serine protease enzyme chymotrypisin relative to structurally related members of this class.     

雄激素非依赖前列腺癌细胞系代谢组学的初步研究

探讨雄激素依赖性前列腺癌LNCaP细胞系向雄激素非依赖性前列腺癌细胞系(LNCaP-AI和LNCaP-AI+F)转变过程的代谢组学变化,寻找前列腺癌发生雄激素耐药的可能发生机制.利用超高效液相色谱-四极杆-飞行时间质谱,在电喷雾电离源在正离子模式下,采用60%(V/V)甲醇-0.85%(w/V)NH4HCO3溶液在-4...     

基于冠心病心肌缺血血瘀证小型猪血清核磁共振代谢组学的研究

通过左冠状动脉前降支放置Ameriod环制备冠心病慢性心肌缺血动物模型,并结合冠脉造影等方法确立中医血瘀证证候,采用现代核磁共振(NMR)和模式识别技术,分析冠心病心肌缺血血瘀证模型与假手术组小型猪4星期血清的共振氢谱,及相应代谢物谱群的变化,开展中医血瘀证候学的研究.结果显示,该方法制备的模型4星期后确立为稳定的冠心...