An intelligentized strategy for endogenous small molecules characterization and quality evaluation of earthworm from two geographic origins by ultra-high performance HILIC/QTOF MSE and Progenesis QI

Comprehensive Analysis of Bile Medicines Based on UHPLC-QTOF-MSE and Machine Learning

Based on UHPLC-QTOF-MSE analysis and quantized processing, combined with machine learning algorithms, data modeling was carried out to realize digital identification of bear bile powder (BBP), chicken bile powder (CIBP), duck bile powder (DBP), cow bile powder (CBP), sheep bile powder (SBP), pig bile powder (PBP), snake bile powder (SNBP), rabbit bile powder (RBP), and goose bile powder (GBP). First, 173 batches of bile samples were analyzed by UHPLC-QTOF-MSE to obtain the retention time-exact mass (RTEM) data pair to identify bile acid-like chemical components. Then, the data were modeled by combining support vector machine (SVM), random forest (RF), artificial neural network (ANN), gradient boosting (GB), AdaBoost (AB), and Naive Bayes (NB), and the models were evaluated by the parameters of accuracy (Acc), precision (P), and area under the curve (AUC). Finally, the bile medicines were digitally identified based on the optimal model. The results showed that the RF model constructed based on the identified 12 bile acid-like chemical constituents and random forest algorithm is optimal with ACC, P, and AUC > 0.950. In addition, the accuracy of external identification verification of 42 batches of bile medicines detected at different times is 100.0%. So based on UHPLC-QTOF-MSE analysis and combined with the RF algorithm, it can efficiently and accurately realize the digital identification of bile medicines, which can provide reference and assistance for the quality control of bile medicines. In addition, hyodeoxycholic acid, glycohyodeoxycholic acid, and taurochenodeoxycholic acid, and so forth are the most important bile acid constituents for the identification of nine bile medicines.

Identification Analysis of Angelicae sinensis radix and Angelicae pubescentis radix Based on Quantized "Digital Identity" and UHPLC-QTOF-MSE Analysis

Angelicae sinensis radix (ASR) and Angelicae pubescentis radix (APR), as traditional herbal medicines, are often confused and doped in the material market. However, the traditional identification method is to characterize the whole herb with a single or a few components, which do not have representation and cannot realize the effective utilization of unknown components. Consequently, the result is not convincing. In addition, the whole process is time-consuming and labor-intensive. To avoid the confusion and adulteration of ASR and APR as well as to strengthen quality control and improve identification efficiency, in this study, a UHPLC-QTOF-MSE method was used to analyze ASR and APR. Based on digital representation, the shared data with high ionic strength were extracted from different batches of the same herbal medicine as their "digital identity". Further, the above "digital identity" was used as the benchmark for matching and identifying unknown samples to feedback on matching credibility (MC). The results showed that based on the "digital identities" of ASR and APR, the digital identification of two herbal samples can be realized efficiently and accurately at the individual level. And the matching credibility (MC) was higher than 94.00%, even if only 1% of APR or ASR in the mixed samples can still be identified efficiently and accurately. The study is of great practical significance for improving the efficiency of the identification of ASR and APR, cracking down on adulterated and counterfeit drugs, and strengthening the quality control of ASR and APR. In addition, it has important reference significance for developing nontargeted digital identification of herbal medicines at the individual level based on UHPLC-QTOF-MSE and "digital identity", which is beneficial to the construction of digital Chinese medicine and digital quality control.

Digital identification and adulteration analysis of Pulsatilla Radix and Pulsatilla Cernua based on "digital identity" and UHPLC-QTOF-MSE

Under the background of digitalization of traditional Chinese medicine (TCM), to realize the quick identification and adulteration analysis of Pulsatilla Radix (PR), adhering to digital conviction, this study conducted UHPLC-QTOF-MSE analysis on PR and its adulterant-Pulsatilla Cernua (PC) from different batches and based on digital conversion, the shared ions were extracted from different batches of PR and PC as their "ions representation", respectively. Further, the data set of unique ions of PR relative to PC and PC relative to PR were screened out as the "digital identities" of PR and PC respectively. Further, above the "digital identities" of PR and PC were used as the benchmarks for matching and identifying to feedback give a matching credibility (MC). The results showed that based on the "digital identities" of PR and PC, the digital identification of two herbal samples can be realized efficiently and accurately at the individual level with the MC≥70.00 %, even if 5 % of PC in the mixed samples can still be identified efficiently and accurately. The study is of great practical significance for improving the identification efficiency of PR and PC, cracking down on adulterated and counterfeit drugs, and strengthening the quality control of PR. In addition, it has important reference significance for developing non-targeted digital identification of herbal medicines at the individual level based on UHPLC-QTOF-MSE and the "digital identity", which was beneficial to the construction of digital Chinese medicine and digital quality control.

Differential Chemical Components Analysis of Periplocae Cortex, Lycii Cortex, and Acanthopanacis Cortex Based on Mass Spectrometry Data and Chemometrics

Background:Periplocae Cortex (PC), Acanthopanacis Cortex (AC), and Lycii Cortex (LC), as traditional Chinese medicines, are all dried root bark, presented in a roll, light and brittle, easy to break, have a fragrant scent, etc. Due to their similar appearances, it is tough to distinguish them, and they are often confused and adulterated in markets and clinical applications. To realize the identification and quality control of three herbs, in this paper, Ultra Performance Liquid Chromatography-Quadrupole Time of Flight Mass Spectrometry Expression (UHPLC-QTOF-MSE) combined with chemometric analysis was used to explore the different chemical compositions. Methods: LC, AC, and PC were analyzed by UHPLC-QTOF-MSE, and the quantized MS data combined with Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) were used to explore the different chemical compositions with Variable Importance Projection (VIP) > 1.0. Further, the different chemical compositions were identified according to the chemical standard substances, related literature, and databases. Results: AC, PC, and LC can be obviously distinguished in PCA and PLS-DA analysis with the VIP of 2661 ions > 1.0. We preliminarily identified 17 differential chemical constituents in AC, PC, and LC with significant differences (p < 0.01) and VIP > 1.0; for example, Lycium B and Periploside H2 are LC and PC's proprietary ingredients, respectively, and 2-Hydroxy-4-methoxybenzaldehyde, Periplocoside C, and 3,5-Di-O-caffeoylquinic acid are the shared components of the three herbs. Conclusions: UHPLC-QTOF-MSE combined with chemometric analysis is conducive to exploring the differential chemical compositions of three herbs. Moreover, the proprietary ingredients, Lycium B (LC) and Periploside H2 (PC), are beneficial in strengthening the quality control of AC, PC, and LC. In addition, limits on the content of shared components can be set to enhance the quality control of LC, PC, and AC.

Characterization of Meat Metabolites and Lipids in Shanghai Local Pig Breeds Revealed by LC-MS-Based Method

The meat of local livestock breeds often has unique qualities and flavors. In this study, three Shanghai native pig breeds (MSZ, SWT, and SHB) exhibited better meat quality traits than globalized commercial pig breeds (DLY). Subsequently, metabolomic and lipidomic differences in the longissimus dorsi (L) and gluteus (T) muscles of the Shanghai native pig breeds and DLY pig breed were compared using liquid chromatography-mass spectrometry (LC-MS). The results demonstrated that the metabolites mainly consisted of (28.16%) lipids and lipid-like molecules, and (25.87%) organic acids and their derivatives were the two most dominant groups. Hundreds of differential expression metabolites were identified in every compared group, respectively. One-way ANOVA was applied to test the significance between multiple groups. Among the 20 most abundant differential metabolites, L-carnitine was significantly different in the muscles of the four pig breeds (p-value = 7.322 × 10-11). It was significantly higher in the L and T muscles of the two indigenous black pig breeds (MSZ and SWT) than in the DLY pigs (p-value < 0.001). Similarly, lipidomic analysis revealed the PA (18:0/18:2) was significantly more abundant in the muscle of these two black breeds than that in the DLY breed (p-value < 0.001). These specific metabolites and lipids might influence the meat quality and taste properties and lead to customer preferences. Therefore, this study provided insights into the characterization of meat metabolites and lipids in Shanghai native pig breeds.

2-(2-Phenylethyl)chromones increase in Aquilaria sinensis with the formation of agarwood

Obtained from Aquilaria Lam. and Gyrinops Gaertn., agarwood is a prestigious perfume and medicinal material in the world. Its primary chemical constituents and indicators of agarwood's development are 2-(2-phenylethyl)chromones (PECs). However, how PECs affect its quality, accumulation, and transformation pattern is still unclear. The present study investigated this issue by monitoring resin filling in agarwood generated by the whole-tree agarwood-inducing technique over a span of a year, observing the ethanol extract concentration at different sampling times, and statistically examining PECs in agarwood from each sampling period. In agarwood, the resin accumulated over time, except during the 4th-6th month due to the creation of a barrier layer. The relative content of total PECs demonstrated an overall increase throughout the year but a decrease from the 4th month to the 6th month, and the relative content of 19 PECs that persisted throughout the year was positively correlated with the content of ethanol extracts. In addition, the process of chromone accumulation was accompanied by the production and transformation of different types of chromones, with flindersia type 2-(2-phenylethyl)chromones, epoxy-2-(2-phenylethyl)chromones, and diepoxy-2-(2-phenylethyl)chromones being the major chromone components; in addition, the content of 5,6,7,8-tetrahydro-2-(2-phenylethyl)chromones kept increasing after 6 months of agarwood formation. Three main trends were identified from 58 analogs of PECs, each with notable variation. The first type had the highest content at the beginning of resin formation. The second type had the highest content at 6 months and then started to decrease, and the third type had a slowly increasing content. As a whole, this study systematically investigated the accumulation of PECs during injury-induced agarwood production in A. sinensis, which is of scientific significance in resolving the transformation of PECs and revealing the secret of agarwood formation.

A Comprehensive Analysis of Fel Ursi and Its Common Adulterants Based on UHPLC-QTOF-MSE and Chemometrics

BACKGROUND

As one of the four most valuable animal medicines, Fel Ursi, named Xiong Dan (XD) in China, has the effect of clearing heat, calming the liver, and brightening the eyes. However, due to the special source of XD and its high price, other animals' bile is often sold as XD or mixed with XD on the market, seriously affecting its clinical efficacy and consumers' rights and interests. In order to realize identification and adulteration analysis of XD, UHPLC-QTOF-MSE and multivariate statistical analysis were used to explore the differences in XD and six other animals' bile.

METHODS

XD, pig gall (Zhu Dan, ZD), cow gall (Niu Dan, ND), rabbit gallbladder (Tu Dan, TD), duck gall (Yan Dan, YD), sheep gall (Yang Dan, YND), and chicken gall (Ji Dan, JD) were analyzed by UHPLC-QTOF-MSE, and the MS data, combined with multivariate analysis methods, were used to distinguish between them. Meanwhile, the potential chemical composition markers that contribute to their differences were further explored.

RESULTS

The results showed that XD and six other animals' bile can be distinguished from each other obviously, with 27 ions with VIP > 1.0. We preliminarily identified 10 different bile acid-like components in XD and the other animals' bile with significant differences (p < 0.01) and VIP > 1.0, such as tauroursodeoxycholic acid, Glycohyodeoxycholic acid, and Glycodeoxycholic acid.

CONCLUSIONS

The developed method was efficient and rapid in accurately distinguishing between XD and six other animals' bile. Based on the obtained chemical composition markers, it is beneficial to strengthen quality control for bile medicines.

Geographical region traceability of wild topmouth culter (Culter alburnus) from Xingkai Lake based on muscle quality and aroma profiles

The wild topmouth culter (Culter alburnus) from Xingkai Lake (XKL) is highly regarded for its delicious taste and unique flavor. In this study, based on muscle quality and aroma analysis, we first differentiated the XKL population from three wild populations in Heilongjiang Province and one artificially cultured population (from Xingkai Lake). Compared with the other populations, the XKL population has a significantly higher crude protein content, essential amino acid content, delicious amino acid content, and n-3/n-6 PUFA ratio. Additionally, it exhibits superior hardness, elasticity, chewiness, recoverability, and viscosity. E-nose detection analysis revealed that W1S, W2S, and W3S were the potential sensors contributing the most to the differences among the five populations. HS-SPME-GC-MS and multivariate regression analysis showed that 21 volatile flavor compounds were identified as key markers for geographical identification of the Xingkai Lake region. These findings will provide guidance for the geographical traceability and identification of the XKL population.

Molecular formula assignment of dissolved organic matter by ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry using two non-targeted data processing approaches: A case study from recirculating aquaculture systems

BACKGROUND

The accumulation of dissolved organic matter (DOM) poses an issue in the management of the water quality from recirculating aquaculture systems (RAS), but its characterization is often not detailed enough to understand the DOM transformations in RAS. In this study, we investigated the application of two distinct non-targeted data processing approaches using ultra-performance liquid chromatography (UPLC) with quadrupole time-of-flight mass spectrometry (QTOF-MS) and two software with different algorithmic designs: PetroOrg and Progenesis QI to accurately characterize the molecular composition of DOM in RAS by UPLC-QTOF-MS.

RESULTS

The UPLC-QTOF-MS resolution in combination with PetroOrg and Progenesis QI software successfully assigned 912 and 106 unique elemental compositions, respectively, including compounds containing carbon, hydrogen, and oxygen (CHO) and nitrogen-containing CHO compounds (CHON), in the DOM samples from RAS. The results of these two distinct data processing approaches were consistent with the list of DOM formulas from RAS identified by higher resolution mass spectrometry techniques confirming their reliability. PetroOrg approach revealed only compositional information in the DOM samples from RAS, while Progenesis QI in addition to identifying new elemental compositions, increased their chemical space by giving information about their polarity and their possible key structures. DOM samples from RAS were found to be rich in unsaturated CHO compounds, with tentatively key structures of terpenoids with medium polarity indicating natural origins in their composition. The analysis also revealed probable structures of sucrose fatty acid esters and polyethylene glycol, indicating anthropogenic sources.

SIGNIFICANCE AND NOVELTY

The combination of these two non-targeted data processing approaches significantly improves the characterization of the complex mixture of DOM from RAS by UPLC-QTOF-MS reporting for the first time accurate DOM results in terms of its composition, while proposing its key structures. The presented methods can also be used to analyze different DOM samples with other HRMS techniques and software.

Urine and serum metabolomic analysis of endometrial cancer diagnosis and classification based on ultra-performance liquid chromatography mass spectrometry

OBJECTIVE

This study aimed to reveal the urinary and serum metabolic pattern of endometrial cancer (EC) and establish diagnostic models to identify EC from controls, high-risk from low-risk EC, and type II from type I EC.

METHOD

This study included 146 EC patients (comprising 79 low-risk and 67 high-risk patients, including 124 type I and 22 type II) and 59 controls. The serum and urine samples were analyzed using ultraperformance liquid chromatography mass spectrometry. Analysis was used to elucidate the distinct metabolites and altered metabolic pathways. Receiver operating characteristic (ROC) analyses were employed to discover and validate the potential biomarker models.

RESULTS

Serum and urine metabolomes displayed significant differences between EC and controls, with metabolites related to amino acid and nicotinamide metabolisms. The serum and urine panels distinguished these two groups with Area Under the Curve (AUC) of 0.821 and 0.902, respectively. The panel consisting of serum and urine metabolites demonstrated the best predictive ability (AUC = 0.953 and 0.976 in discovering and validation group). In comparing high-risk and low risk EC, differential metabolites were enriched in purine and glutamine metabolism. The AUC values for serum and urine panels were 0.818, and 0.843, respectively. The combined panel exhibited better predictive accuracy (0.881 in discovering group and 0.936 in external validation). In the comparison between type I and type II group, altered folic acid metabolism was identified. The serum, urine and combined panels discriminated these two groups with the AUC of 0.829, 0.913 and 0.922, respectively.

CONCLUSION

The combined urine and serum metabolome effectively revealed the metabolic patterns in EC patients, offering valuable diagnostic models for EC diagnosis and classification.

Urine metabolomics for assessing fertility-sparing treatment efficacy in endometrial cancer: a non-invasive approach using ultra-performance liquid chromatography mass spectrometry

OBJECTIVE

This study aimed to reveal the urine metabolic change of endometrial cancer (EC) patients during fertility-sparing treatment and establish non-invasive predictive models to identify patients with complete remission (CR).

METHOD

This study enrolled 20 EC patients prior to treatment (PT) and 22 patients with CR, aged 25-40 years. Eligibility criteria consisted of stage IA high-grade EC, lesions confined to endometrium, normal hepatic and renal function, normal urine test, no contraindication for fertility-sparing treatment and no prior therapy. Urine samples were analyzed using ultraperformance liquid chromatography mass spectrometry (UPLC-MS), a technique chosen for its high sensitivity and resolution, allows for rapid, accurate identification and quantification of metabolites, providing a comprehensive metabolic profile and facilitating the discovery of potential biomarkers. Analytical techniques were employed to determine distinct metabolites and altered metabolic pathways. The statistical analyses were performed using univariate and multivariate analyses, logistic regression and receiver operating characteristic (ROC) curves to discover and validate the potential biomarker models.

RESULTS

A total of 108 different urine metabolomes were identified between CR and PT groups. These metabolites were enriched in ascorbate and aldarate metabolism, one carbon pool by folate, and some amino acid metabolisms pathways. A panel consisting of Baicalin, 5beta-1,3,7 (11)-Eudesmatrien-8-one, Indolylacryloylglycine, Edulitine, and Physapubenolide were selected as biomarkers, which demonstrated the best predictive ability with the AUC values of 0.982/0.851 in training/10-fold-cross-validation group, achieving a sensitivity of 0.975 and specificity of 0.967, respectively.

CONCLUSION

The urine metabolic analysis revealed the metabolic changes in EC patients during the fertility-sparing treatment. The predictive biomarkers present great potential diagnostic value in fertility-sparing treatments for EC patients, offering a less invasive means of monitoring treatment efficacy. Further research should explore the mechanistic underpinnings of these metabolic changes and validate the biomarker panel in larger, diverse populations due to the small sample size and single-institution nature of our study.

Characterization of natural peptides in Pheretima by integrating proteogenomics and label-free peptidomics

Pheretima, also called "earthworms", is a well-known animal-derived traditional Chinese medicine that is extensively used in over 50 Chinese patent medicines (CPMs) in Chinese Pharmacopoeia (2020 edition). However, its zoological origin is unclear, both in the herbal market and CPMs. In this study, a strategy for integrating in-house annotated protein databases constructed from close evolutionary relationship-sourced RNA sequencing data from public archival resources and various sequencing algorithms (restricted search, open search, and de novo) was developed to characterize the phenotype of natural peptides of three major commercial species of Pheretima, including Pheretima aspergillum (PA), Pheretima vulgaris (PV), and Metaphire magna (MM). We identified 10,477 natural peptides in the PA, 7,451 in PV, and 5,896 in MM samples. Five specific signature peptides were screened and then validated using synthetic peptides; these demonstrated robust specificity for the authentication of PA, PV, and MM. Finally, all marker peptides were successfully applied to identify the zoological origins of Brain Heart capsules and Xiaohuoluo pills, revealing the inconsistent Pheretima species used in these CPMs. In conclusion, our integrated strategy could be used for the in-depth characterization of natural peptides of other animal-derived traditional Chinese medicines, especially non-model species with poorly annotated protein databases.

LC-MS based urine untargeted metabolomic analyses to identify and subdivide urothelial cancer

Introduction

Urine metabolomics has been a promising technique in the liquid biopsy of urothelial cancer (UC). The comparison of upper tract urothelial cancer (UTUC), lower tract urothelial cancer (BCa), and healthy controls (HCs) need to be performed to find related biomarkers.

Methods

In our investigation, urine samples from 35 UTUCs, 44 BCas, and 53 gender- and age-matched HCs were analyzed using liquid chromatography-high resolution mass spectrometry (LC-HRMS). In different groups, the differential metabolites and the disturbed metabolism pathways were explored. Transcriptomics and urine metabolomics are combined to identify the probably disturbed gene in BCa.

Results

With an area under the curve (AUC) of 0.815, the panel consisting of prostaglandin I2, 5-methyldeoxycytidine, 2,6-dimethylheptanoyl carnitine, and deoxyinosine was able to discriminate UC from HCs. With an AUC of 0.845, the validation group also demonstrated strong predictive ability. UTUC and BCa without hematuria could be distinguished using the panel of 5'-methylthioadenosine, L-beta-aspartyl-L-serine, dehydroepiandrosterone sulfate, and N'-formylkynurenine (AUC=0.858). The metabolite panel comprising aspartyl-methionine, 7-methylinosine, and alpha-CEHC glucuronide could discriminate UTUC from BCa with hematuria with an AUC of 0.83. Fatty acid biosynthesis, purine metabolism, tryptophan metabolism, pentose and glucuronate interconversions, and arachidonic acid metabolism were dysregulated when comparing UC with HCs. PTGIS and BCHE, the genes related to the metabolism of prostaglandin I2 and myristic acid respectively, were significantly associated with the survival of BCa.

Discussion

Not only could LC-HRMS urine metabolomic investigations distinguish UC from HCs, but they could also identify UTUC from BCa. Additionally, urine metabolomics combined with transcriptomics can find out the potential aberrant genes in the metabolism.

Identification of Daphne genkwa and Its Vinegar-Processed Products by Ultraperformance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry and Chemometrics

Crude herbs of Daphne genkwa (CHDG) are often used in traditional Chinese medicine to treat scabies baldness, carbuncles, and chilblain owing to their significant purgation and curative effects. The most common technique for processing DG involves the use of vinegar to reduce the toxicity of CHDG and enhance its clinical efficacy. Vinegar-processed DG (VPDG) is used as an internal medicine to treat chest and abdominal water accumulation, phlegm accumulation, asthma, and constipation, among other diseases. In this study, the changes in the chemical composition of CHDG after vinegar processing and the inner components of the changed curative effects were elucidated using optimized ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Untargeted metabolomics, based on multivariate statistical analyses, was also used to profile differences between CHDG and VPDG. Eight marker compounds were identified using orthogonal partial least-squares discrimination analysis, which indicated significant differences between CHDG and VPDG. The concentrations of apigenin-7-O-β-d-methylglucuronate and hydroxygenkwanin were considerably higher in VPDG than those in CHDG, whereas the amounts of caffeic acid, quercetin, tiliroside, naringenin, genkwanines O, and orthobenzoate 2 were significantly lower. The obtained results can indicate the transformation mechanisms of certain changed compounds. To the best of our knowledge, this study is the first to employ mass spectrometry to detect the marker components of CHDG and VPDG.

A comparison of feature extraction capabilities of advanced UHPLC-HRMS data analysis tools in plant metabolomics

Data analysis of ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) is an essential and time-consuming step in plant metabolomics and feature extraction is the fundamental step for current tools. Various methods lead to different feature extraction results in practical applications, which may puzzle users for selecting adequate data analysis tools to deal with collected data. In this work, we provide a comprehensive method evaluation for some advanced UHPLC-HRMS data analysis tools in plant metabolomics, including MS-DIAL, XCMS, MZmine, AntDAS, Progenesis QI, and Compound Discoverer. Both mixtures of standards and various complex plant matrices were specifically designed for evaluating the performances of the involved method in analyzing both targeted and untargeted metabolomics. Results indicated that AntDAS provide the most acceptable feature extraction, compound identification, and quantification results in targeted compound analysis. Concerning the complex plant dataset, both MS-DIAL and AntDAS can provide more reliable results than the others. The method comparison is maybe useful for the selection of suitable data analysis tools for users.

Metabolomics meets systems immunology

Metabolic processes play a critical role in immune regulation. Metabolomics is the systematic analysis of small molecules (metabolites) in organisms or biological samples, providing an opportunity to comprehensively study interactions between metabolism and immunity in physiology and disease. Integrating metabolomics into systems immunology allows the exploration of the interactions of multilayered features in the biological system and the molecular regulatory mechanism of these features. Here, we provide an overview on recent technological developments of metabolomic applications in immunological research. To begin, two widely used metabolomics approaches are compared: targeted and untargeted metabolomics. Then, we provide a comprehensive overview of the analysis workflow and the computational tools available, including sample preparation, raw spectra data preprocessing, data processing, statistical analysis, and interpretation. Third, we describe how to integrate metabolomics with other omics approaches in immunological studies using available tools. Finally, we discuss new developments in metabolomics and its prospects for immunology research. This review provides guidance to researchers using metabolomics and multiomics in immunity research, thus facilitating the application of systems immunology to disease research.

Urine metabolites for preoperative prediction of acute kidney injury after coronary artery bypass graft surgery

OBJECTIVE

Acute kidney injury is a common complication after on-pump coronary artery bypass grafting. Prediction of acute kidney injury remains a challenge. Our study aims to identify a panel of urine metabolites for preoperative warning of acute kidney injury after on-pump coronary artery bypass grafting.

METHODS

A total of 159 patients undergoing isolated on-pump coronary artery bypass grafting were enrolled from July 7, 2017, to May 17, 2019. Preoperative urine samples were analyzed with the approach of liquid chromatography-mass spectrometry-based urine metabolomics. The study end point was the episode of acute kidney injury within 48 hours postoperatively. The predictive performance was determined by the area under the curve and calibration curve. The results were validated using bootstrap resampling.

RESULTS

The acute kidney injury (n = 55) and nonacute kidney injury (n = 104) groups showed significant different metabolic profiling. A total of 28 metabolites showed significant differences between the acute kidney injury and nonacute kidney injury groups. A metabolite panel of 5 metabolites (tyrosyl-gamma-glutamate, deoxycholic acid glycine conjugate, 5-acetylamino-6-amino-3-methyluracil, arginyl-arginine, and L-methionine) was discovered to have a good predicting performance (area under the curve, 0.89; 95% confidence interval, 0.82-0.93), which is higher than the clinical factor-based model (area under the curve, 0.63; 95% confidence interval, 0.53-0.72). Internal validation by bootstrap resampling showed an adjusted area under the curve of 0.88, and the calibration curve demonstrated good agreement between prediction and observation in the probability of postoperative acute kidney injury. Decision curve analysis revealed a superior net benefit of the metabolite model over the traditional clinical factor-based model.

CONCLUSIONS

We present 5 urine metabolites related to acute kidney injury after coronary artery bypass grafting. This metabolite model may serve as a preoperative warning of acute kidney injury after on-pump coronary artery bypass grafting.

Bio-organic fertilizers improve Dendrocalamus farinosus growth by remolding the soil microbiome and metabolome

Organic and microbial fertilizers have potential advantages over inorganic fertilizers in improving soil fertility and crop yield without harmful side-effects. However, the effects of these bio-organic fertilizers on the soil microbiome and metabolome remain largely unknown, especially in the context of bamboo cultivation. In this study, we cultivated Dendrocalamus farinosus (D. farinosus) plants under five different fertilization conditions: organic fertilizer (OF), Bacillus amyloliquefaciens bio-fertilizer (Ba), Bacillus mucilaginosus Krassilnikov bio-fertilizer (BmK), organic fertilizer plus Bacillus amyloliquefaciens bio-fertilizer (OFBa), and organic fertilizer plus Bacillus mucilaginosus Krassilnikov bio-fertilizer (OFBmK). We conducted 16S rRNA sequencing and liquid chromatography/mass spectrometry (LC-MS) to evaluate the soil bacterial composition and soil metabolic activity in the different treatment groups. The results demonstrate that all the fertilization conditions altered the soil bacterial community composition. Moreover, the combination of organic and microbial fertilizers (i.e., in the OFBa and OFBmK groups) significantly affected the relative abundance of soil bacterial species; the largest number of dominant microbial communities were found in the OFBa group, which were strongly correlated with each other. Additionally, non-targeted metabolomics revealed that the levels of soil lipids and lipid-like molecules, and organic acids and their derivatives, were greatly altered under all treatment conditions. The levels of galactitol, guanine, and deoxycytidine were also markedly decreased in the OFBa and OFBmK groups. Moreover, we constructed a regulatory network to delineated the relationships between bamboo phenotype, soil enzymatic activity, soil differential metabolites, and dominant microbial. The network revealed that bio-organic fertilizers promoted bamboo growth by modifying the soil microbiome and metabolome. Accordingly, we concluded that the use of organic fertilizers, microbial fertilizers, or their combination regulated bacterial composition and soil metabolic processes. These findings provide new insights into how D. farinosus-bacterial interactions are affected by different fertilization regiments, which are directly applicable to the agricultural cultivation of bamboo.

An Integrated Strategy of Chemical Fingerprint and Network Pharmacology for the Discovery of Efficacy-Related Q-Markers of Pheretima

Pheretima, one of the animal-derived traditional Chinese medicines, has been wildly used in various cardiovascular and cerebrovascular diseases, including stroke, coronary heart disease, hyperlipidemia, and hyperglycemia. However, it was still a big challenge to select the quality markers for Pheretima quality control. The fingerprint and network pharmacology-based strategy was proposed to screen the efficiency related quality markers (Q-Markers) of Pheretima. The ratio of sample to liquid, ultrasonic-extraction time, temperature, and power were optimized by orthogonal design, respectively. The chemical fingerprint of forty batches of Pheretima was established, and six common peaks were screened. The network pharmacology was used to construct the Pheretima-Components-Targets-Pathways-Stroke network. It was found that six potential efficacy Q-markers in Pheretima could exert the relaxing meridians effect to treat stroke through acting on multiple targets and regulating various pathways. A simple HPLC-DAD method was developed and validated to determine the efficacy Q-markers. Grey relational analysis was used to further verify the relation of potential efficiency related quality markers with the anticoagulation activity of Pheretima, which indicated that the contents of these markers exhibited high relationship with the anticoagulation activity. It was concluded that hypoxanthine, uridine, phenylalanine, inosine, guanosine, and tryptophan were selected as quality markers related to relaxing meridians to evaluate the quality of Pheretima. The fingerprint and network pharmacology-based strategy was proved to be a powerful strategy for the discovery of efficiency related Q-markers of Pheretima.

Application of plasma metabolome for monitoring the effect of rivaroxaban in patients with nonvalvular atrial fibrillation

Rivaroxaban, an oral factor Xa inhibitor, has been used to treating a series of thromboembolic disorders in clinical practice. Measurement of the anticoagulant effect of rivaroxaban is important to avoid serious bleeding events, thus ensuring the safety and efficacy of drug administration. Metabolomics could help to predict differences in the responses among patients by profiling metabolites in biosamples. In this study, plasma metabolomes before and 3 hours after rivaroxaban intake in 150 nonvalvular atrial fibrillation (NVAF) patients and 100 age/gender-matched controls were analyzed by liquid chromatography coupled with mass spectrometry (LC-MS/MS). When compared with controls, a total of thirteen plasma metabolites were differentially expressed in the NVAF patients. Pathway analysis revealed that purine and lipid metabolism were dysregulated. A panel of three metabolites (17a-ethynylestradiol, tryptophyl-glutamate and adenosine) showed good predictive ability to distinguish nonvalvular atrial fibrillation with an area under the receiver operating characteristic curve (AUC) of 1 for the discovery phase and 1 for validation. Under rivaroxaban treatment, a total of seven metabolites changed, the lipid and glycosylphosphatidylinositol biosynthesis pathways were altered and the panel consisting of avocadene, prenyl glucoside and phosphatidylethanolamine showed predictive ability with an AUC of 0.86 for the discovery dataset and 0.82 for the validation. The study showed that plasma metabolomic analyses hold the potential to differentiate nonvalvular atrial fibrillation and can help to monitor the effect of rivaroxaban anticoagulation.

Antimicrobial and anticancer activities of Hainan dry noni fruit alcoholic extracts and their novel compounds identification using UPLC-Q-Exactive Obitrap-MS/MS

Morinda citrifolia Linn (noni) is an important plant in the Pacific Asian region. The fruit has been used as a food source and has shown therapeutical benefits for health. Recently, it has become a source for bioactive compounds. In this study, we investigated the antimicrobial and anticancer activities of alcoholic extracts of Hainan dry noni fruit with machinery assistance and identified their novel compounds by UPLC-Q-Exactive Obitrap-MS/MS. By IE extractor aided method, the extraction of both NFE (Noni Fruit Ethanol) and NFM (Noni Fruit Methanol) solvent crude sample extracts were obtained with recovery yields of 98.48% and 71.65%, respectively. The antimicrobial effect of the crude extracts was subjected to disc diffusion test screening against two microbial strains bacterium SA (Staphylococcus aureus) and, fungal CA (Candida albicans). The MIC values of SA and CA were 35.34 and 47.80 mg/mL for NFE, 117.40 and 108.01 mg/mL for NFM, respectively. Further on, cell viability assay showed that IC₅₀ values of extract NFE and NFM on human UMUC-3 bladder carcinogenic cells were 865.1 and 789.1 µg/mL with less effect to human SVHUC-1 normal cell line for 72hr incubation. Using UPLC-Q-exactive Orbitrap-MS/MS, ten compounds were identified in the noni extracts and confirmed from the HMDB and FooDB. Five known bioactive compounds had been used for treatments in anti-cancer, anti-obesity, and Covid-19 patients. The remaining five compounds were found novel in noni fruit. They were Cyanidin 3-(2 G-xylosylrutinoside), Inulobiose, Clausarinol, Pectachol, and 4,7-Megastigmadien-9-ol. The potential bioactivities of these novel compounds will be studied in the near future. These findings form a basis on screening natural medicinal plant extracts for beneficial use as a food and health source.

Rapid characterization of chemical constituents in Naoling Pian by LC-MS combined with data processing techniques

Naoling Pian is a prescription composed of 15 herbs, which is mainly used for the treatment of insomnia in clinical practice. However, the chemical constituents in Naoling Pian are numerous and unclear, which hinders the interpretation of its bioactive constituents and the subsequent research on the material basis for pharmacodynamics. The purpose of this study is to develop a rapid method for identifying the chemical constituents of Naoling Pian using high-throughput ultra-performance liquid chromatography quadrupole time of flight coupled with mass spectrometry combined with a software platform for data processing. The whole composition of Naoling Pian was characterized in positive and negative ion modes. In this experiment, an overall total of 201 constituents were identified by using reference standards, online and self-built databases matching, fragmentation rules analysis of mass spectrometry peaks with a software platform. Meanwhile, Naoling Pian was analyzed for the first time using LC-MS method, the constituents could be identified in a quick and accurate manner, and the results could provide a scientific basis for the follow-up research on the pharmacodynamic material basis and quality control of Naoling Pian. This article is protected by copyright. All rights reserved.

Characterization of LC-MS based urine metabolomics in healthy children and adults

Previous studies reported that sex and age could influence urine metabolomics, which should be considered in biomarker discovery. As a consequence, for the baseline of urine metabolomics characteristics, it becomes critical to avoid confounding effects in clinical cohort studies. In this study, we provided a comprehensive lifespan characterization of urine metabolomics in a cohort of 348 healthy children and 315 adults, aged 1 to 78 years, using liquid chromatography coupled with high resolution mass spectrometry. Our results suggest that sex-dependent urine metabolites are much greater in adults than in children. The pantothenate and CoA biosynthesis and alanine metabolism pathways were enriched in early life. Androgen and estrogen metabolism showed high activity during adolescence and youth stages. Pyrimidine metabolism was enriched in the geriatric stage. Based on the above analysis, metabolomic characteristics of each age stage were provided. This work could help us understand the baseline of urine metabolism characteristics and contribute to further studies of clinical disease biomarker discovery.

Analysis of the saliva metabolic signature in patients with primary Sjögren’s syndrome

Background

The saliva metabolome has been applied to explore disease biomarkers. In this study we characterized the metabolic profile of primary Sjögren’s syndrome (pSS) patients and explored metabolomic biomarkers.

Methods

This work presents a liquid chromatography-mass spectrometry-based metabolomic study of the saliva of 32 patients with pSS and 38 age- and sex-matched healthy adults. Potential pSS saliva metabolite biomarkers were explored using test group saliva samples (20 patients with pSS vs. 25 healthy adults) and were then verified by a cross-validation group (12 patients with pSS vs. 13 healthy adults).

Results

Metabolic pathways, including tryptophan metabolism, tyrosine metabolism, carbon fixation, and aspartate and asparagine metabolism, were found to be significantly regulated and related to inflammatory injury, neurological cognitive impairment and the immune response. Phenylalanyl-alanine was discovered to have good predictive ability for pSS, with an area under the curve (AUC) of 0.87 in the testing group (validation group: AUC = 0.75).

Conclusion

Our study shows that salivary metabolomics is a useful strategy for differential analysis and biomarker discovery in pSS.

Urinary Metabolomic Study in a Healthy Children Population and Metabolic Biomarker Discovery of Attention-Deficit/Hyperactivity Disorder (ADHD)

Objectives

Knowledge of the urinary metabolomic profiles of healthy children and adolescents plays a promising role in the field of pediatrics. Metabolomics has also been used to diagnose disease, discover novel biomarkers, and elucidate pathophysiological pathways. Attention-deficit/hyperactivity disorder (ADHD) is one of the most common psychiatric disorders in childhood. However, large-sample urinary metabolomic studies in children with ADHD are relatively rare. In this study, we aimed to identify specific biomarkers for ADHD diagnosis in children and adolescents by urinary metabolomic profiling.

Methods

We explored the urine metabolome in 363 healthy children aged 1-18 years and 76 patients with ADHD using high-resolution mass spectrometry.

Results

Metabolic pathways, such as arachidonic acid metabolism, steroid hormone biosynthesis, and catecholamine biosynthesis, were found to be related to sex and age in healthy children. The urinary metabolites displaying the largest differences between patients with ADHD and healthy controls belonged to the tyrosine, leucine, and fatty acid metabolic pathways. A metabolite panel consisting of FAPy-adenine, 3-methylazelaic acid, and phenylacetylglutamine was discovered to have good predictive ability for ADHD, with a receiver operating characteristic area under the curve (ROC-AUC) of 0.918. A panel of FAPy-adenine, N-acetylaspartylglutamic acid, dopamine 4-sulfate, aminocaproic acid, and asparaginyl-leucine was used to establish a robust model for ADHD comorbid tic disorders and controls with an AUC of 0.918.

Maltose-functionalized HILIC stationary phase silica gel based on self-assembled oligopeptides and its application for the separation of polar compounds

In this study, carbonyldiimidazole was used to bond maltose-modified oligopeptides (Ala-Glu-Ala-Glu-Ala-Lys-Ala-Lys) to the surface of silica spheres for hydrophilic interaction liquid chromatography (HILIC). Attenuated total reflectance-Fourier transform infrared spectroscopy, elemental analysis, X-ray photoelectron spectroscopy, thermogravimetric analysis, BET technique, and water contact angle measurement results confirmed the successful immobilization of the obtained material. Compared with the conventional method for preparing carbohydrate stationary phases, this method involves simpler steps and less time-consuming processes. The experimental results proved that the retention mechanism of the maltose-based HILIC column matched the typical HILIC retention mechanism. The column showed high separation efficiency and stability toward the separation of polar compounds such as amino acids, bases, nucleosides, water-soluble vitamins, and salicylic acid and its analogs. The column achieved high selectivity toward oligosaccharide separation. In addition, this efficient analysis demonstrates the applicability of the as-prepared material in the field of food inspection.

A rapid and simple signature peptides-based method for species authentication of three main commercial Pheretima

Pheretima with various activities is a commonly used animal-derived traditional medicine in Asia countries. However, almost half of them are non-pharmacopoeia species in the market due to the similar morphological characteristics between medicinal and non-medicinal species. This study aims to establish an effective method based on signature peptides for species authentication of three main commercial Pheretima, including two major Pheretima species (Amynthas aspergillum, Metaphire vulgaris) and one main adulteration (Metaphire magna). Firstly, the species of 52 batches of commercial Pheretima were authenticated based on DNA barcodes. Secondly, proteomic analysis was performed for protein characterization of three main commercial Pheretima. Furthermore, their signature peptides were screened and validated using ultra-high performance liquid chromatography coupled with mass spectrometry (UPLC-MS/MS) in multiple reaction monitoring (MRM) mode. Moreover, a simplified sample processing method was developed. Finally, large quantities of commercial Pheretima samples were analyzed for further verifying the feasibility of the signature peptides-based method. The result showed that the established method had a great application potential for authenticity identification of commercial Pheretima. SIGNIFICANCE: The authenticity assessment of medicinal materials is a main issue in the quality control process as deceptive practices could imply severe health risks. In this study, a rapid and simple method based on signature peptides was established for species authentication of three main commercial Pheretima, which can be an effective alternative to complex DNA barcoding and difficult morphological identification, and provided a reference for improvement of Pheretima quality standards.

Authentication of three main commercial Pheretima based on amino acids analysis

Pheretima has been used as an animal-derived traditional Chinese medicine for thousands of years in Asian countries due to its multi-activities. However, more than half of the commercial Pheretima are adulterants according to the previous research. Besides, the standards of Pheretima are still inadequate in the identification of Pheretima species. In this study, an amino acids (AAs) analytical method established based on the ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-QqQ-MS) in multiple reaction monitoring (MRM) mode through derivatization with 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) was used for qualitative and quantitative analysis of the total AAs of three main commercial Pheretima (two major Pheretima species, Amynthas aspergillum, Metaphire vulgaris, and one main counterfeit, M. magna). As a result, 16 AAs were detected and quantitated in their hydrolyzed samples. Then, multivariate statistical analysis was applied to distinguish the three commercial Pheretima based on their AAs level. Finally, four AAs (Thr, Glu, Asp, and Arg) were screened as species-differential AAs, which may be used as chemical markers to distinguish the three commercial Pheretima. This study deeply described the outline of AAs in Pheretima and offered a good reference for its species authentication.

A systematic review on Zhilong Huoxue Tongyu capsule in treating cardiovascular and cerebrovascular diseases: Pharmacological actions, molecular mechanisms and clinical outcomes

ETHNOPHARMACOLOGICAL RELEVANCE

Cardiovascular and cerebrovascular diseases have become a severe threat for human health worldwide, however, optimal therapeutic options are still developed. Zhilong Huoxue Tongyu capsule (ZL capsule) is mainly composed of Astragalus membranaceus, Leech, Earthworm, Cinnamomum cassia and Sargentodoxa cuneata, having functions of replenishing qi and activating blood, dispelling wind and reducing phlegm. It is an expanded application on the basis of traditional uses of above TCMs, acquiring a satisfactory curative effect on cardiovascular and cerebrovascular diseases over twenty years.

AIM OF THE STUDY

To comprehensively summarize the main components of ZL capsule, understand the mechanisms of ZL capsule, and conclude clinical regimens of ZL capsule for cardiovascular and cerebrovascular diseases.

MATERIALS AND METHODS

We selected network pharmacology technology to analyze main active compounds and predict underlying mechanism of ZL capsule against atherosclerosis. Molecular docking was performed to simulate the interaction pattern between the active components of ZL capsule and putative targets. Further, PubMed, Web of Science, China National Knowledge Infrastructure and Google Scholar were used to search literatures, with the key words of "Zhilong Huoxue Tongyu capsule", "cardiovascular and cerebrovascular diseases", "atherosclerosis", "clinical study" and their combinations, mainly from 2000 to 2020.

RESULTS

Both network pharmacology analysis, molecular docking and animal experiments studies confirmed that mechanisms of ZL capsule plays the role of anti-inflammatory, anti-apoptosis and promoting angiogenesis in treating cardiovascular and cerebrovascular diseases by multi-components acting on multi-targets via multi-pathways. Over 1000 clinical cases were benefited from the treatment of ZL capsule, suggesting a holistic concept of "the same therapy for different myocardial and cerebral diseases".

CONCLUSIONS

For the first time, this systematic review may supply meaningful information for further studies to explore material basis and pharmacodynamics of ZL capsule and also provide a basis for sharing the "Chinese patent medicine" for cardiovascular and cerebrovascular diseases.

Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking

The urine metabolome constitutes a rich source of functional information reflecting physiological states that are influenced by distinct conditions and biological stresses, such as responses to drug treatments or disease manifestations. Although global liquid chromatography-mass spectrometry (MS) profiling provides the most comprehensive measurement of metabolites in complex biological samples, annotation remains a challenge, and computational approaches are necessary to translate the molecular composition into biological knowledge. Here, we investigated the use of tandem MS-based enhanced molecular networks (MolNetEnhancer) to improve the metabolite annotation of urine extracts. The samples (n = 10) were analyzed by hydrophilic interaction chromatography-quadrupole time-of-flight mass spectrometry in both electrospray ionization (ESI) modes. Consistent with other common data preprocessing software, the use of Progenesis QI led to the annotation of up to 20 metabolites based on MS2 library searches, showing a high fragmentation score (cosine similarity ≥ 0.7), that is, ∼2% of mass features containing MS2 spectra. Molecular networking based on library matching resulted in the annotation of up to 62 urinary compounds. Using a combination of unsupervised substructure discovery (MS2LDA), the in silico tool network annotation propagation (NAP), and ClassyFire chemical ontology, embedded in a multilayered molecular network by MolNetEnhancer, we were able to expand the chemical characterization to ∼50% of the data set. The integrative approach led to the annotation of 275 compounds at the metabolomics standards initiative (MSI) confidence level 2, as well as 459 and 578 urinary metabolites (MSI level 3) in both negative and positive ESI modes, respectively. The exhaustive MS2-based annotation outperformed similar studies applied to larger cohorts while offering the discovery of metabolites not identified by the MS2 library search. This is the first work that effectively integrates orthogonal annotation methods and MS2-based fragmentation studies to improve metabolite annotation in urine samples.

The global profiling of alkaloids in Aconitum stapfianum and analysis of detoxification material basis against Fuzi

Aconitum alkaloids are versatile in chemical structures and are well known for their bioactivity and toxicity. Cases of analogs with closely similar structures or positional isomers are widespread in herbs of the Aconitum genus. It is still challenging to rapidly identify unknown compounds via mass spectrometry, especially positional isomers. Herein, to profile the alkaloids of Aconitum stapfianum that possess bioactivity against intoxication by the lateral root of Aconitum carmichaelii (Fuzi), a strategy was developed by carefully determining the fragmentation pathways of authentic standards. A series of rules was summarized and involved charge site effects, hydrogen bonding effects, competitive channels between charge-remote reactions and charge migration reactions, and fragment patterns exhibiting a "diamond shape". Accordingly, a total of 124 alkaloids in A. stapfianum were tentatively characterized, including 85 potential new compounds and 24 sets of isomers. On the other hand, to explore the material basis of detoxification, a chemical constituent comparison was made between A. stapfianum and Fuzi, and principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were performed to identify markers that were different between the two . In total, 25 characteristic markers were identified to discriminate between these two herbal medicines, of which 14 compounds were specific for A. stapfianum and most of them were characteristic for a para-substituted benzoic acid ester at C-14.

Mass spectrometry-based serum lipidomics strategy to explore the mechanism of Eleutherococcus senticosus (Rupr. & Maxim.) Maxim. leaves in the treatment of ischemic stroke

Eleutherococcus senticosus (Rupr. & Maxim.) Maxim. leaves (ESL) were reported to have neuroprotective function and are also used to treat cranial and cerebral traumas as a traditional Chinese medicine and food herbage plant. However, there has been no previous study on ESL treatment for stroke at the level of lipid disorders. To clarify the mechanism of ESL in treating ischemic stroke, this study was carried out from 3 aspects, namely, the regulation of lipid disorders, protection of the nervous system, as well as anti-inflammatory and antioxidant actions. This study established a lipidomics research strategy that was developed by UPLC-Q-TOF/MS analysis. The quantification of neurotransmitters in the serum and brain tissue of rats was performed using UPLC-TQ/MS. Also, we quantified the oxidative stress and inflammatory reaction by measuring the contents of SOD, MDA, TNF-α, IL-6, and IL-10 via the ELISA kits for serum and brain tissue. According to UPLC-Q-TOF/MS-based lipidomics analysis, 27 lipidomics biomarkers were identified in this study, including PC, PE, SM, and TG, which were distributed in various lipid metabolic pathways, including glycerophospholipid, linoleic acid, alpha-linolenic acid, glycerolipid, sphingolipid, and arachidonic acid metabolism pathways. By reversing the changes in the lipid content caused by the disease, ESL has a therapeutic effect on ischemic stroke. Furthermore, quantitative results of neurotransmitters indicated that they can be regulated by ESL. Finally, the results of ELISA showed that ESL can treat ischemic stroke to a certain extent by reducing the oxidative and inflammatory damage. Therefore, ESL may play a therapeutic role in the treatment of ischemic stroke in different ways. This research preliminarily revealed the mechanism of ESL in the treatment of ischemic stroke and provided support for the further application of ESL.

Chemical profiling and multicomponents quantitative analysis of Panzerina lanata by ultra-fast liquid chromatography with tandem mass spectrometry

Panzerina lanata is a Chinese medicine with the bioactivity of detumescence and detoxification. In this study, novel qualitative and quantitative methods were established by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry and ultra-high-performance liquid chromatography-triple quadrupole linear ion trap mass spectrometry, respectively. As a result, 20 compounds were identified or tentatively characterized including flavonoids, organic acids, alkaloids, and lignans, five of which were identified for the first time based on the reference standards. The quantitative approach exhibited good linearity (R²  > 0.995), precision (RSDs < 4.97%), stability (RSDs < 4.77%), and recovery (96.04-104.14%). Afterward, this method was implemented to determine 11 flavonoids in four batches of P. lanata. Among them, seven compounds were quantified for the first time. Narcissin was abundant in each batch of P. lanata (average of 10.890-14.230 mg/g) with the highest quantities. The results provide valuable information for quality evaluation.

Marker peptide screening and species-specific authentication of Pheretima using proteomics

Pheretima is a common and valuable animal-derived medication used in traditional Chinese medicine. There are four species of Pheretima specified in the Chinese Pharmacopoeia (2015 edition), i.e. Pheretima aspergillum, P. vulgaris, P. guillelmi, and P. pectinifera. A recent report revealed ~ 55% of Pheretima in the commercial marketplace may be adulterated by other species, contrary to the Pharmacopoeia standard. The safety, efficacy, and authenticity of Pheretima is an important issue. Currently, the availability of specific quality-markers for the various species and effective identification methods are still limited. In this study, label-free quantification proteomics of species from Pheretima and Amynthas was carried out using nanoscale liquid chromatography coupled to tandem mass spectrometry (nano LC-MS/MS), and marker peptides were identified based on their ion intensities using multivariate data analysis (principal component analysis and supervised partial least-squares discriminant analysis). A total of 48,476 peptides with high confidence corresponding to 13,397 proteins were identified from all samples. The marker peptides were validated by comparison with synthetic peptide reference standards using LC-MS/MS operating in a multiple-reaction monitoring mode. A multiple-peptide identification strategy was proposed for the authentication of Pheretima and subsequently applied to samples obtained from retail outlets in various regions of China. The results showed that eight out of the 15 samples tested were deemed authentic Pheretima.

Different Metabolites in the Roots, Seeds, and Leaves of Acanthopanax senticosus and Their Role in Alleviating Oxidative Stress

In this study, we examined the metabolites from different parts of Acanthopanax senticosus and their role in alleviating damage caused by oxidative stress. We used UHPLC-QTOF-MS to analyze the chemical components in the root, seed, and leaf extracts of A. senticosus. Two multivariate statistical analysis methods-namely, principal component analysis and partial least square discriminant analysis-were used to distinguish the samples obtained from different parts of the plant. Using univariate statistics, 130 different metabolites were screened out. Among these, the relative content of flavonoids and terpenoids was found to be highest in the leaves, the lignin and phenolic acid content was highest in the roots, and the amino acid and phenolic acid levels were highest in seeds. An MTT assay was used to test the anti-H₂O₂ oxidative damage to PC12 cells in different parts of the sample. Lastly, using Pearson's correlation analysis, various metabolites from different parts of A. senticosus were correlated with their antioxidant effects from the corresponding parts. Fifty-two related different metabolites were found, of which 20 metabolites that were positively correlated to oxidative stress were present at a relatively higher level in the roots, whereas 32 metabolites that were negatively correlated were present at relatively higher levels in the seeds and leaves. The results of this study reveal the distribution characteristics and the antioxidant activity of different metabolites of A. senticosus and provide a reference for the rational development of its medicinal parts.

A comprehensive quality evaluation of Fuzi and its processed product through integration of UPLC-QTOF/MS combined MS/MS-based mass spectral molecular networking with multivariate statistical analysis and HPLC-MS/MS

ETHNOPHARMACOLOGICAL RELEVANCE

Aconiti Lateralis Radix Praeparata (the Chinese name is Fuzi, FZ), the lateral or daughter root of Aconitum carmichaelii Debx. (Ranunculaceae), is a controversial traditional Chinese medicine (TCM) that is universally distributed and applied in many countries, such as China, Japan, Korea, and India. FZ can be used to treat various diseases, including rheumatic fever, rheumatism, painful joints, syncope, collapse, bronchial asthma, some endocrinal disorders, etc. However, quality control and assessment of FZ are challenging due to its obvious and high toxicological risks, and only its processed products are allowed to be used clinically according to the relative safety regulations. Consequently, it is necessary to analyze the whole chemical composition and the dynamic changes of FZ before and after processing. Addressing the changes in the chemical substance of raw and processed products is a way to reduce toxicity.

AIM OF THE STUDY

In this article, the whole chemical composition of FZ is analyzed, the differences between raw and processed FZ are evaluated, and possible factors that influence the reduced toxicity of processed FZ are explained from the perspective of its chemical composition using qualitative and quantitative analysis methods.

MATERIALS AND METHODS

A novel strategy of multiple data collection and processing based on ultra-performance liquid chromatography coupled with a quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) method in the positive ion mode, together with Global Natural Product Social Molecular Networking (GNPS) and multivariate statistical analysis, was established to systematically identify the chemical constituents of FZ and comprehensively investigate the chemical markers that can be used to differentiate FZ processed with vinegar and honey from its raw product. Combined with the qualitative analysis results, 12 components, including 8 chemical marker compounds and 4 toxicity components, were quantitatively analyzed by using high-performance liquid chromatography equipped with triple-quadrupole mass spectrometry (HPLC-MS/MS).

RESULTS

Using the molecular networking (MN) analysis method, a total of 145 compounds were identified, of which 13 were identified using reference compounds. Seventy seven chemical markers were also detected between raw and processed FZ. The identification results of the chemical markers were also verified by orthogonal partial least squares discriminant analysis (OPLS-DA). The quantitative results indicated that the contents of 12 important components all decreased, especially diester-diterpenoid alkaloids (DDAs), after processing.

CONCLUSION

The decrease of toxicity of FZ after processing is closely related to the changes in its chemical composition. The method developed in this study is a comprehensive analysis technique for quality assessment of FZ, and this study provides a useful and quick strategy to characterize chemical compounds of TCM and explore the different chemical markers between raw and processed Chinese herbal medicine.

Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection

BACKGROUND

Due to its prevalence and negative impacts on both the economy and society, the diabetes mellitus (DM) has emerged as a worldwide concern. In light of this, the label-free quantification (LFQ) proteomics and diabetic marker selection methods have been applied to elucidate the underlying mechanisms associated with insulin resistance, explore novel protein biomarkers, and discover innovative therapeutic protein targets.

OBJECTIVE

The purpose of this manuscript is to review and analyze the recent computational advances and development of label-free quantification and diabetic marker selection in diabetes proteomics.

METHODS

Web of Science database, PubMed database and Google Scholar were utilized for searching label-free quantification, computational advances, feature selection and diabetes proteomics.

RESULTS

In this study, we systematically review the computational advances of label-free quantification and diabetic marker selection methods which were applied to get the understanding of DM pathological mechanisms. Firstly, different popular quantification measurements and proteomic quantification software tools which have been applied to the diabetes studies are comprehensively discussed. Secondly, a number of popular manipulation methods including transformation, pretreatment (centering, scaling, and normalization), missing value imputation methods and a variety of popular feature selection techniques applied to diabetes proteomic data are overviewed with objective evaluation on their advantages and disadvantages. Finally, the guidelines for the efficient use of the computationbased LFQ technology and feature selection methods in diabetes proteomics are proposed.

CONCLUSION

In summary, this review provides guidelines for researchers who will engage in proteomics biomarker discovery and by properly applying these proteomic computational advances, more reliable therapeutic targets will be found in the field of diabetes mellitus.

Urinary metabolomic investigations in vitiligo patients

Urinary metabolomics is a useful non-invasive tool for large-scale screening of disease-related metabolites. However, no comprehensive urinary metabolomic analysis of vitiligo is presently available. To investigate the urine metabolic pattern of vitiligo patients, we conducted a combined cross-sectional and prospective self-control cohort study and an untargeted urinary metabolomic analysis. In the cross-sectional study, 295 vitiligo patients and 192 age‐ and sex‐matched controls were enrolled, and 71 differential metabolites between two groups were identified. Pathway enrichment analysis revealed that drug metabolism-cytochrome P450, biopterin metabolism, vitamin B9 (folate) metabolism, selenoamino acid metabolism, and methionine and cysteine metabolism showed significant enrichment in vitiligo patients compared with the status in healthy controls. In the self-control cohort, 46 active vitiligo patients were recruited to analyse the urinary metabolic signatures after treatment. All of these patients were asked to undertake follow-up visits every 2 months three times after first consulting and the disease stage was evaluated compared with that at the last visit. Folate metabolism, linoleate metabolism, leukotriene metabolism, alkaloid biosynthesis, and tyrosine metabolism were predicted to be involved in vitiligo activity. Our study is the first attempt to reveal urinary metabolic signatures of vitiligo patients and provides new insights into the metabolic mechanisms of vitiligo.

Comprehensive profiling of the chemical components and potential markers in raw and processed Cistanche tubulosa by combining ultra-high-performance liquid chromatography coupled with tandem mass spectrometry and MS/MS-based molecular networking

Chinese materia medica processing is a distinguished and unique pharmaceutical technique in traditional Chinese medicine (TCM), which has played an important role in reducing side effects, increasing medical potencies, altering the properties and even changing the curative effects of raw herbs. The efficacy improvement in medicinal plants is mainly caused by changes in the key substances through an optimized processing procedure. Thus, the use of a rapid method for determining suitable chemical markers between raw and processed TCM is critical in order to elucidate how the bioactive compounds influence the clinical effects. In this study, ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry combined with MS/MS-based molecular networking (MN) and a multivariate statistical analysis method is proposed for the first time. This combination was used to identify the complex chemical composition and clarify the changed constituents between raw and processed Cistanche tubulosa (C. tubulosa). The chemical analysis results demonstrated that a total of 85 compounds were identified in the crude and processed C. tubulosa. Moreover, 34 compounds were detected as chemical markers. This systematic research into chemical constituents and chemical markers of crude and processed C. tubulosa lays a solid foundation for further study of the quality control of C. tubulosa. Moreover, the study provides a new and valuable technical strategy for analyzing chemical components and identifying potential chemical markers for the processing of herbal medicines.Graphical abstract.

Investigation of Plasma Metabolic and Lipidomic Characteristics of a Chinese Cohort and a Pilot Study of Renal Cell Carcinoma Biomarker

Plasma metabolomics and lipidomics have been commonly used for biomarker discovery. Studies in white and Japanese populations suggested that gender and age can affect circulating plasma metabolite profiles; however, the metabolomics characteristics in Chinese population has not been surveyed. In our study, we applied liquid chromatography-mass spectrometry-based approach to analyze Chinese plasma metabolome and lipidome in a cohort of 534 healthy adults (aging from 15 to 79). Fatty-acid metabolism was found to be gender- and age-dependent in Chinese, similar with metabolomics characteristics in Japanese and white populations. Differently, lipids, such as TGs and DGs, were found to be gender-independent in Chinese population. Moreover, nicotinate and nicotinamide metabolism was found to be specifically age-related in Chinese. The application of plasma metabolome and lipidome for renal cell carcinoma diagnosis (143 RCC patients and 34 benign kidney tumor patients) showed good accuracy, with an area under the curve (AUC) of 0.971 for distinction from healthy control, and 0.839 for distinction from the benign. Bile acid metabolism was found to be related to RCC probably combination with intestinal microflora. Definition of the variation and characteristics of Chinese normal plasma metabolome and lipidome might provide a basis for disease biomarker analysis.

Thrombin-based discovery strategy of bioactive-chemical quality marker combination for pollen of Typha orientalis by metabolomics coupled with chemometrics

BACKGROUND

It is of utmost significance to choose the bioactive components as quality markers for ensuring the effectiveness of traditional Chinese medicine (TCM). Nonetheless, some markers are able to assess effectively the quality of TCM without considering the pharmacological mechanisms and intrinsic chemical complexities.

OBJECTIVE

This underscores the need to discover new and efficient markers which can assess both quality and mechanism of action. Herein, a strategy of bioactive-chemical quality marker combination was proposed to improve the level of the quality control of TCM by metabolomics coupled with chemometrics.

METHODS

A four-step plan was followed. Firstly, acquisition of metabolic features and component characterization of different batches of pollen of Typha orientalis C.Presl were performed using UHPLC-Q-TOF/MS. Secondly, the direct inhibitory effects of pollen of T. orientalis on thrombin was assessed by using chromogenic substrate method together with HPLC. Thereafter, bioactive-chemical marker combination associated with anti-thrombin segregation was screened using supervised classifiers. Finally, quantitative assay and prediction-model of selected markers were established for guarantying the quality of pollen of T. orientalis.

RESULTS

A total of 22 compounds were annotated based on comparison with previous work from pollen of T. orientalis by UHPLC-Q-TOF/MS. Citric acid and linolenic acid inhibited the thrombin activity with IC₅₀ values, 0.52 ± 0.02 and 0.51 ± 0.02 mg/mL, respectively. A bioactive-chemical marker combination including citric acid, linolenic acid, typhaneoside, and isorhamnetin-3-O-neohesperidoside were discovered and selected as quality markers for evaluation of pollen of T. orientalis according to their capacity for inhibiting thrombin.

CONCLUSION

The thrombin-based discovery strategy of bioactive-chemical marker combination was a powerful tool for screening the quality markers for evaluation of pollen of T. orientalis.

Plasma leptin level mirrors metabolome alterations in young adults

INTRODUCTION

Leptin is known to regulate pathways of energy metabolism, reproduction, and control appetite. Whether plasma leptin levels reflect changes in metabolites of these pathways is unknown.

OBJECTIVES

We aimed to find whether there is an association between leptin levels and levels of metabolites of energy and hormone metabolism.

METHODS

We performed an untargeted metabolomics analysis of plasma from 110 healthy adults (men: women = 1:1; aged 18-40 years), using liquid chromatography-tandem mass spectrometry. Blood samples were collected from all the study subjects in the fasting state. Clinical features and markers of obesity and Type 2 diabetes mellitus (T2DM) were assessed in all. The association between levels of metabolites and clinical and biochemical parameters was identified using the multivariable-adjusted linear regression model and PLS-DA analysis.

RESULTS

The leptin level was found to have a significant association with a substantial number of metabolites in women and men. Leptin level was positively associated with glycocholic acid and arachidic acid, metabolites related to energy metabolisms, pregnanediol-3-glucuronide, a metabolite of progesterone metabolism, and quercetin 3'-sulfate, a diet-derived metabolite. Leptin level was negatively associated with ponasteroside A and barringtogenol C levels. Leptin level was positively correlated with adiponectin and negatively with total calorie intake and levels of triglyceride and very-low-density lipoprotein. Leptin levels were associated with lipid and sex hormone metabolism in women, while metabolites involved in amino acid metabolism were correlated to leptin in men.

CONCLUSION

Our study indicates that leptin level reflects metabolome alterations and hence could be a useful marker to detect early changes in energy and hormone metabolisms.

Metabolomics study of the hepatoprotective effect of Phellinus igniarius in chronic ethanol-induced liver injury mice using UPLC-Q/TOF-MS combined with ingenuity pathway analysis

BACKGROUND

Phellinus igniarius (L.) Quèl as a potential medicinal mushroom possesses multiple biological activities including hepatoprotection, but the hepatoprotective mechanism is not clear.

PURPOSE

To elucidate the hepatoprotective effect and potential target of P. igniarius.

METHODS

The male C57BL/6 mice were fed with the Lieber-DeCarli diet containing alcohol or isocaloric maltose dextrin as control diet with or without P. igniarius decoction (PID) in the dosage of 0.65 g/kg and 2.6 g/kg. The levels of serum biomarkers were detected by an automatic biochemistry analyser. The histopathological changes of liver were observed by hematoxylin and eosin (H&E) staining. Ultra performance liquid chromatography-quadrupole/time-of-flight mass spectrometry (UPLC-Q/TOF-MS) was applied for investigating the dynamic changes of serum metabolites in chronic ethanol-induced liver injury mice and after treatment with PID. Ingenuity pathway analysis (IPA) was employed to identify the potential target of PID.

RESULTS

PID could significantly reduce the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), triglyceride (TG) and total bile acid (TBA) in serum and improved hepatic steatosis and inflammation. In terms of metabolism, a total of 36 serum differential metabolites were identified, and PID intervention regulated 24 of them, involving the key metabolic pathways such as the biosynthesis of unsaturated fatty acids, primary bile acid biosynthesis, glycerophospholipid metabolism, fatty acids biosynthesis, ether lipid metabolism and arachidonic acid metabolism. On the mechanism, IPA showed that farnesol X receptor (FXR) was the major potential target for PID, and PID could improve chronic alcohol intake induced by the inhibition of mRNA expression of FXR in the liver and the activation of mRNA expression of FXR in the intestine in mice.

CONCLUSION

The present study for the first time systematically illustrated the hepatoprotective effect of P. igniarius and preliminarily explored its potential target FXR. P. igniarius might be exploited as a promising therapeutic option for alcoholic liver injury.

LC-MS-Based Plasma Metabolomics and Lipidomics Analyses for Differential Diagnosis of Bladder Cancer and Renal Cell Carcinoma

Bladder cancer (BC) and Renal cell carcinoma(RCC) are the two most frequent genitourinary cancers in China. In this study, a comprehensive liquid chromatography-mass spectrometry (LC-MS) based method, which utilizes both plasma metabolomics and lipidomics platform, has been carried out to discriminate the global plasma profiles of 64 patients with BC, 74 patients with RCC, and 141 healthy controls. Apparent separation was observed between cancer (BC and RCC) plasma samples and controls. The area under the receiving operator characteristic curve (AUC) was 0.985 and 0.993 by plasma metabolomics and lipidomics, respectively (external validation group: AUC was 0.944 and 0.976, respectively). Combined plasma metabolomics and lipidomics showed good predictive ability with an AUC of 1 (external validation group: AUC = 0.99). Then, separation was observed between the BC and RCC samples. The AUC was 0.862, 0.853 and 0.939, respectively, by plasma metabolomics, lipidomics and combined metabolomics and lipidomics (external validation group: AUC was 0.802, 0.898, and 0.942, respectively). Furthermore, we also found eight metabolites that showed good predictive ability for BC, RCC and control discrimination. This study indicated that plasma metabolomics and lipidomics may be effective for BC, RCC and control discrimination, and combined plasma metabolomics and lipidomics showed better predictive performance. This study would provide a reference for BC and RCC biomarker discovery, not only for early detection and screening, but also for differential diagnosis.

UPLC-MS based urine untargeted metabolomic analyses to differentiate bladder cancer from renal cell carcinoma

Background

To discover biomarker panels that could distinguish cancers (BC and RCC) from healthy controls (HCs) and bladder cancers (BC) from renal cell carcinoma (RCC), regardless of whether the patients have haematuria. In addition, we also explored the altered metabolomic pathways of BC and RCC.

Methods

In total, 403 participants were enrolled in our study, which included 146 BC patients (77 without haematuria and 69 with haematuria), 115 RCC patients (94 without haematuria and 21 with haematuria) and 142 sex- and age-matched HCs. Their midstream urine samples were collected and analysed by performing UPLC-MS. The statistical methods and pathway analyses were applied to discover potential biomarker panels and altered metabolic pathways.

Results

The panel of α-CEHC, β-cortolone, deoxyinosine, flunisolide, 11b,17a,21-trihydroxypreg-nenolone and glycerol tripropanoate could distinguish the patients with cancer from the HCs (the AUC was 0.950) and the external validation also displayed a good predictive ability (the AUC was 0.867). The panel of 4-ethoxymethylphenol, prostaglandin F2b, thromboxane B3, hydroxybutyrylcarnitine, 3-hydroxyphloretin and N′-formylkynurenine could differentiate BC from RCC without haematuria. The AUC was 0.829 in the discovering group and 0.76 in the external validation. The metabolite panel comprising 1-hydroxy-2-oxopropyl tetrahydropterin, 1-acetoxy-2-hydroxy-16-heptadecyn-4-one, 1,2-dehydrosalsolinol and L-tyrosine could significantly discriminate BC from RCC with haematuria (AUC was 0.913). Pathway analyses revealed altered lipid and purine metabolisms between cancer patients and HCs, together with disordered amino acid and purine metabolisms between BC and RCC with haematuria.

Conclusions

UPLC-MS urine metabolomic analyses could not only differentiate cancers from HCs but also discriminate BC from RCC. In addition, pathway analyses demonstrated a deeper metabolic mechanism of BC and RCC.

Eurotium Cristatum Fermented Okara as a Potential Food Ingredient to Combat Diabetes

Type 2 diabetes mellitus (T2DM) is a chronic disease, and dietary modification is a crucial part of disease management. Okara is a sustainable source of fibre-rich food. Most of the valorization research on okara focused more on the physical attributes instead of the possible health attributes. The fermentation of okara using microbes originated from food source, such as tea, sake, sufu and yoghurt, were explored here. The aim of this study is to investigate fermented okara as a functional food ingredient to reduce blood glucose levels. Fermented and non-fermented okara extracts were analyzed using the metabolomic approach with UHPLC-QTof-MS^E. Statistical analysis demonstrated that the anthraquinones, emodin and physcion, served as potential markers and differentiated Eurotium cristatum fermented okara (ECO) over other choices of microbes. The in-vitro α-glucosidase activity assays and in-vivo mice studies showed that ECO can reduce postprandial blood glucose levels. A 20% ECO loading crispy snack prototype revealed a good nutrition composition and could serve as a fundamental formulation for future antidiabetes recipe development, strengthening the hypothesis that ECO can be used as a novel food ingredient for diabetic management.