Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification.

Isobaric labeling-based proteomics is widely applied in deep proteome quantification. Among the platforms for isobaric labeled proteomic data analysis, the commercial software Proteome Discoverer (PD) is widely used, incorporating the search engine CHIMERYS, while FragPipe (FP) is relatively new, free for noncommercial purposes, and integrates the engine MSFragger. Here, we compared PD and FP over three public proteomic data sets labeled using 6plex, 10plex, and 16plex tandem mass tags. Our results showed the protein abundances generated by the two software are highly correlated. PD quantified more proteins (10.02%, 15.44%, 8.19%) than FP with comparable NA ratios (0.00% vs. 0.00%, 0.85% vs. 0.38%, and 11.74% vs. 10.52%) in the three data sets. Using the 16plex data set, PD and FP outputs showed high consistency in quantifying technical replicates, batch effects, and functional enrichment in differentially expressed proteins. However, FP saved 93.93%, 96.65%, and 96.41% of processing time compared to PD for analyzing the three data sets, respectively. In conclusion, while PD is a well-maintained commercial software integrating various additional functions and can quantify more proteins, FP is freely available and achieves similar output with a shorter computational time. Our results will guide users in choosing the most suitable quantification software for their needs.

Proteomics and metabolomics analyses reveal the full spectrum of inflammatory and lipid metabolic abnormalities in dyslipidemia.

Dyslipidemia is a common, chronic metabolic disease associated with cardiovascular complications. Due to the multiplicity of etiological factors, the pathogenesis of dyslipidemia is still unclear. In this study, we combined proteomics and metabolomics methods to analyze the plasma of patients with dyslipidemia and healthy subjects. isobaric tags for relative and absolute quantification (iTRAQ) markers, combined with LC-MS/MS proteomics technology and the UHPLC/Orbitfast-X Tribrid system, were used to establish the metabolite profile in clinical dyslipidemia. A total of 137 differentially expressed proteins, mainly related to biological processes such as protein activation cascades, adaptive immune responses, complement activation, acute inflammatory responses, and regulation of acute inflammatory responses, were identified. These proteins are involved in the regulation of important metabolic pathways, such as immunity and inflammation, coagulation and hemostasis, lipid metabolism, and oxidation and antioxidant defenses. The analysis of clinical metabolites showed there were 69 different metabolites in plasma, mainly related to glycerolipid, sphingolipid, porphyrin, α-linolenic acid, linoleic acid, and arachidonic acid metabolism, suggesting that the regulation of inflammation and lipid metabolism may be disturbed in patients with dyslipidemia. Among these, significant changes were observed in indole-3-propionic acid (IPA), which is considered as a potential biomarker of dyslipidemia. The combined analysis of proteins and metabolites showed that arachidonic acid, linoleic acid, and lipid metabolic pathways were closely related to dyslipidemia. IPA may be a potential biomarker. The information provided in this study may provide new insights into the pathogenesis of animal models of dyslipidemia and related disease models, as well as potential intervention targets.

Multiomics-based dissection of citrus flavonoid metabolism using a Citrus reticulata × Poncirus trifoliata population.

Deciphering the genetic basis of plant secondary metabolism will provide useful insights for genetic improvement and enhance our fundamental understanding of plant biological processes. Although citrus plants are among the most important fruit crops worldwide, the genetic basis of secondary metabolism in these plants is largely unknown. Here, we use a high-density linkage map to dissect large-scale flavonoid metabolic traits measured in different tissues (young leaf, old leaf, mature pericarp, and mature pulp) of an F1 pseudo-testcross citrus population. We detected 80 flavonoids in this population and identified 138 quantitative trait loci (QTLs) for 57 flavonoids in these four tissues. Based on transcriptional profiling and functional annotation, twenty-one candidate genes were identified, and one gene encoding flavanone 3-hydroxylase (F3H) was functionally verified to result in naturally occurring variation in dihydrokaempferol content through genetic variations in its promoter and coding regions. The abundant data resources collected for diverse citrus germplasms here lay the foundation for complete characterization of the citrus flavonoid biosynthetic pathway and will thereby promote efficient utilization of metabolites in citrus quality improvement.

Parallel Metabolomic and Transcriptomic Analysis Reveals Key Factors for Quality Improvement of Tea Plants.

As one of the most popular beverages globally, tea has enormous economic, cultural, and medicinal importance that necessitates a comprehensive metabolomics study of this species. In this study, a large-scale targeted metabolomics analysis on two types of leaf tissues of nine tea cultivars from five representative geographical origins within China was carried out using the liquid chromatography-mass spectrometry technique. RNA-seq-based transcriptomic analysis was in parallel conducted on the same samples, and gene expression and metabolic differentiation between tissues as well as between the multiple tea cultivars were investigated. The data obtained provide an accessible resource for further studies of naturally occurring metabolic variation of tea plants, which will aid in thoroughly interpreting the underlying genetic and molecular mechanisms of biosynthesis of specialized metabolites in this critical species. Candidate genes including a transcription factor (CsMYB5-like), which were highly correlated with both the content of flavonoids and the expression level of genes participating in the phenylpropanoid and flavonoid biosynthesis pathway, were identified as potential targets for quality improvement of tea.

Metabolomics-based parallel discovery of xenobiotics and induced endogenous metabolic dysregulation in clinical toxicology.

Intoxication by xenobiotics triggers the perturbation of metabolic fingerprints in biofluids, including the accumulation of xenobiotic compounds and the dysregulation of endogenous metabolites. In this work, an untargeted metabolomics workflow was developed to simultaneously profile both xenobiotic and endogenous metabolites for the identification of the xenobiotic origin and an in-depth understanding of the intoxication mechanism. This workflow was demonstrated in a real-world clinical case. Plasma samples were collected from four intoxicated children and another three healthy children. Untargeted metabolomics analysis was performed using ultraperformance liquid chromatography (UPLC) coupled to a high-resolution mass spectrometer (HRMS) with data-independent MSE acquisition. LC-MSE data was processed using an untargeted metabolomics data interpretation workflow, in which the identities of xenobiotics and altered endogenous metabolic features were determined via database searching. Five xenobiotic chemicals and 19 endogenous metabolites were found to be dysregulated. Combined with the clinical evidence, penfluridol was confirmed as the xenobiotic toxin. Furthermore, a mechanistic hypothesis was developed to explain the dysregulation of the four endogenous acyl-carnitines. This workflow can be readily applied to a wide range of clinical toxicology cases, offering a powerful and convenient means of simultaneous discovery of intoxication source and the understanding of intoxication mechanisms.

Gut Microbiota and Relevant Metabolites Analysis in Alcohol Dependent Mice.

Alcohol abuse is a major public health crisis. Relative evidences supported that the gut microbiota (GM) played an important role in central nervous system (CNS) function, and the composition of them had changed after alcohol drinking. We sought to explore the changes of GM in alcohol dependence. In our study, the GM of mice with alcohol administration was detected through analyzed 16S rRNA gene sequencing and the fecal metabolites were analyzed by LC-MS. The microbial diversity was significantly higher in the alcohol administration group, the abundance of phylum Firmicutes and its class Clostridiales were elevated, meanwhile the abundance of Lachnospiraceae, Alistipes, and Odoribacter showed significant differences among the three groups. Based on LC-MS results, bile acid, secondary bile acid, serotonin and taurine level had varying degrees of changes in alcohol model. From paraffin sections, tissue damage was observed in liver and colon. These findings provide direct evidence that alcohol intake affects the composition of GM, enable a better understanding of the function of GM in the microbiota-gut-brain (MGB) axis, and give a new thought for alcohol addiction treatment.

[Quality evaluation of Rhei Radix et Rhizoma decoction].

Decoction of single medicinal herb is a reference for the standardization of different dosage forms of Chinese medicine and it provides a new direction for solving the problems existing in the quality of Chinese medicinal granules such as no uniform dosage form and no clear quality standard. In this paper, the quality evaluation method of standard decoction of rhubarb was established to provide reference for the quality control of common dosage forms such as clinical decoction and formula granule. 10 batches of representative Rhei Radix et Rhizoma were collected to establish UPLC fingerprints were established. The chemical structures of main peaks were identified with ultra-performance liquid chromatography with quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and the main components in the decoction were Anthraquinones. The extraction ratio of the standard decoction was (28.1±3.8)% and the transfer rate was (19.9±6.3)%. The method for the quality evaluation of standard decoction of Rhei Radix et Rhizoma was established in this study, providing reference for the quality control method of terminal products from decoction of Rhei Radix et Rhizoma.

[Quality evaluation of decoction of single medicinal herb--a case of Lonicerae Japinicae Flos].

Decoction of single medicinal herb is a reference for the standardization of different dosage form of Chinese medicine and it provides a new direction for solving the problems existing in the quality of Chinese medicinal granules such no uniform dosage forms and no clear quality standard. There are few reports on the idea, method and preparation of single herb standard decoction. Our country is in urgent need of that information in order to improve the consistency and stability of traditional Chinese medicine products. Here, Lonicerae Japinicae Flos was selected as an example to elucidate the preparation and quality evaluation of Chinese single herbal medicine decoction. Twelve batches of representative Lonicerae Japinicae Flos were collected, UPLC fingerprints were established, and the chemical structures of main peaks were identified with UPLC-QTOF-MS and standard compounds. The main components in the decoction are organic acids and iridoids. The extract rate of the standard decoction was (34.2±2.9)% and the transfer rate is (78.6±8.4)% in the form of chlorogenic acid, within the range of 75%-125% of mean. This paper established a method for the quality evaluation of standard decoction of Lonicerae Japinicae Flos and provided reference for the quality control method of terminal products from decoction of Lonicerae Japinicae Flos.

[Establish quality evaluation method based on standard decoction of Danshen extract].

The quality of Danshen extract granules on market is largely different from each other mainly due to the heterogeneous quality of raw materials of Salvia miltiorrhiza, various producing procedures and lack of good quality evaluation method. Formula granule and "standard decoction" have the same quality. In this paper, a systematic evaluation method for the quality of Danshen decoction was established from the perspective of "standard decoction", in order to explore the main factors affecting the quality uniformity of Danshen extract granules. Danshen standard decoction was prepared; then the fingerprint method was developed to determine the content of salvianolic acid B; and the main peaks in the fingerprint were identified with UPLC-QTOF/MS to clarify the chemical compositions of Danshen decoction. Three indexes were calculated to evaluate the stability of whole process, including the extraction ratio; transfer rate of index components and pH value. The results showed that the main components of Danshen decoction were phenolic acids, while the extraction rate, the transfer rate of salvianolic acid B and pH value were in a relatively stable level, and the similarity in the fingerprint of standard decoction was high, indicating that the preparation procedure was stable. The level of salvianolic acid B in the standard decoction was in a large range, which was mainly due to the difference in the quality of Salviae Miltiorrhizae Radix et Rhizoma.

[Establish quality evaluation system for standard Ephedrae Herba decoction].

To establish the quality control methods for the standard decoction of Ephedrae Herba, and provide the reference for quality evaluation method of all Chinese herbal medicine decoction.Standard decoction of Ephedrae Herba was prepared, and UPLC-UV fingerprint was established to determine the total contents of ephedrine and pseudoephedrine. Then UPLC-QTOF/MS was used to confirm the major common peaks in the fingerprint to clarify the main chemical constituents in the decoction. In addition, the stability of the process was evaluated by calculating the parameters such as the extraction ratio, transfer rate of the index components and the pH values.In the decoction of Ephedrae Herba, the total average concentration of ephedrine and pseudoephedrine was (2.11±0.70) g•L⁻¹; the similarities of all the fingerprints were more than 0.85; there were 10 major common peaks in the fingerprint, including alkaloids, flavonoids and organic acids; the extraction ratio was (17±3.2)%, and the overall transfer rate of ephedrine and pseudoephedrine was (32.4±8.1)%.The method for evaluating the quality of standard decoction of Ephedrae Herba was established in this article, providing reference for the quality control of products which were stemmed from the water extract of Ephedrae Herba.

Serum and Brain Metabolomic Variations Reveal Perturbation of Sleep Deprivation on Rats and Ameliorate Effect of Total Ginsenoside Treatment.

Sleep loss or sleep deprivation (SD) refers to shorter sleep than average baseline need, and SD has been a serious problem of modern societies which affects health and well-being. Panax ginseng is a well-known traditional Chinese medicine (TCM). Our previous study has demonstrated that total ginsenosides (GS), the extracts from Panax ginseng, could effectively improve cognition and behavior on SD rats. However, little is known about its metabolomic study. In this study, serum and brain metabolomic method based on gas chromatography coupled with mass spectrometry (GC/MS) was employed to evaluate the efficacy and study the mechanism of GS on a rat model of SD. With pattern recognition analysis of serum and brain tissue metabolite profile, a clear separation of the model group and control group was acquired for serum and brain tissue samples; the MGS (model + GS) group showed a tendency of recovering when compared to control group, which was consistent with behavioral and biochemical parameters. 39 and 40 potential biomarkers of brain tissues and serum samples, respectively, were identified and employed to explore the possible mechanism. Our work revealed that GS has significant protective effects on SD, and metabolomics is a useful tool for evaluating efficacy and elucidating mechanism in TCM.

Rapid Characterization of Constituents in Tribulus terrestris from Different Habitats by UHPLC/Q-TOF MS.

A strategy for rapid identification of the chemical constituents from crude extracts of Tribulus terrestris was proposed using an informatics platform for the UHPLC/Q-TOF MSE data analyses. This strategy mainly utilizes neutral losses, characteristic fragments, and in-house library to rapidly identify the structure of the compounds. With this strategy, rapid characterization of the chemical components of T. terrestris from Beijing, China was successfully achieved. A total of 82 steroidal saponins and nine flavonoids were identified or tentatively identified from T. terrestris. Among them, 15 new components were deduced based on retention times and characteristic MS fragmentation patterns. Furthermore, the chemical components of T. terrestris, including the other two samples from Xinjiang Uygur Autonomous region, China, and Rome, Italy, were also identified with this strategy. Altogether, 141 chemical components were identified from these three samples, of which 39 components were identified or tentatively identified as new compounds, including 35 groups of isomers. It demonstrated that this strategy provided an efficient protocol for the rapid identification of chemical constituents in complex samples such as traditional Chinese medicines (TCMs) by UHPLC/Q-TOF MSE with informatics platform. Graphical Abstract ᅟ.

Screening and identification of hepatotoxic component in Evodia rutaecarpa based on spectrum-effect relationship and UPLC-Q-TOFMS.

Evodia rutaecarpa (E. rutaecarpa) has been used to treat aches, vomiting and dysentery in traditional Chinese medicine. However, as a mildly toxic herb its toxic components have not been elucidated. An attempt was made to illuminate the hepatotoxic constituents of E. rutaecarpa. The 50% ethanol extracts of E. rutaecarpa from 19 different sources were used to establish UPLC fingerprints and administered to mice at a dose of 35 g/kg (crude medicine weight/mouse weight) once daily for 14 days. Serum levels of alanine transaminase, aspartate aminotransferase and liver coefficient were used as indices of liver injury. Additionally, the characteristic peaks of 19 fingerprints were identified. Spectrum-effect relationships between fingerprints and hepatotoxic indicators were analyzed using bivariate correlation analysis (BCA). The UPLC fingerprints were established and a total of 28 main compounds were identified. Because of the inherent variations in chemical compositions, the liver injury levels were different among the E. rutaecarpa samples from 19 sites of production. BCA results indicated that compounds dihydrorutaecarpine, 6-acetoxy-5-epilimonin, goshuyuamide I, 1-methyl-2-[(Z)-5-undecenyl]-4(1H)-quinolone, 1-methyl-2-[(4Z,7Z)-4,7-tridecadienyl]-4(1H)-quinolone, evocarpine and 1-methyl-2-[(6Z,9Z)-6,9-pentadecadienyl]-4(1H)-quinolone were tentatively determined as the primary hepatotoxic components. The present study provides a valuable method for the discovery of hepatotoxic constituents by combination of fingerprints and hepatotoxicity index.

Screening antitumor bioactive fraction from Sauromatum giganteum (Engl.) Cusimano & Hett and sensitive cell lines with the serum pharmacology method and identification by UPLC-TOF-MS.

Sauromatum giganteum (Engl.) Cusimano & Hett Tuber are used in Chinese folklore medicine for treatment of neoplasms. However, the claim has not been scientifically validated. The aim of the study is to screen the antitumor bioactive fraction of Sauromatum giganteum (Engl.) Cusimano & Hett Tuber and sensitive tumor cell lines using a cytotoxicity assay in vitro and tumor transplantation method in vivo, to support its use in folk medicine. The petroleum ether fraction, chloroform fraction, ethyl acetate fraction, n-butanol fraction and water fraction were successively extracted by turn by the maceration under reflux assay. Screening of antitumor bioactive fraction and sensitive cell lines were measured by MTT assay and the serum pharmacology method, and in vivo the antitumor activities of the active fraction was evaluated by using S180 or H22 tumor-bearing mice model and Kunming mice. The active constituents of ethyl acetate fraction of Sauromatum giganteum (Engl.) Cusimano & Hett were characterized by UPLC-TOF-MS. Compared with control groups, mice serum containing ethyl acetate fraction had a inhibition effect on SMMC-7721 cell, SGC-7901 cell, MCF-7 cell, HeLa cell, A549 cell, HT-29, and MDA-MB-231, respectively, but mice serum containing other four fractions had no different with that of control group. The inhibition capabilities of mice serum containing ethyl acetate fraction on the seven cell lines in descending order is SGC-7901 > SMMC-7721 > MCF-7 > HT-29 > A549 > HeLa > MDA-MB-231. In vivo the inhibition rate of 106, 318, 954 mg/kg·d ethyl acetate fraction dry extract to sarcoma S180 is 15.22%, 26.15% and 40.24%, respectively, and life prolonging rate to hepatoma H22 is 33.61%, 40.16% and 55.74%. A total of 14 compounds were identified in the ethyl acetate fraction of Sauromatum giganteum (Engl.) Cusimano & Hett. The results of the experimental studies proved the antitumor activity of Sauromatum giganteum (Engl.) Cusimano & Hett and supported the traditional use of this plant. These data indicate the potential for the use of ethyl acetate fraction of Sauromatum giganteum (Engl.) Cusimano & Hett Tuber in tumor therapy, anti-tumor activity on cancer cell line in descending order is SGC-7901 > SMMC-7721 > MCF-7 > HT-29 > A549 > HeLa > MDA-MB-231.

[Qualitative analysis of chemical constituents in Si-Wu Decoction based on TCM component database].

In order to clarify the chemical constituents of Si-Wu Decoction rapidly and holistically, we analyzed the ethanol extract of Si-Wu Decoction by UPLC/Q-TOF-MSE and UNIFI which based on traditional Chinese medicine database, the probable structures of 113 compounds were identified. The results show that this method can rapidly and effectively characterize the chemical compounds of Si-Wu Decoction and provide a new solution for identification of components from complex TCM extract.

Transcriptomic and metabonomic profiling reveal synergistic effects of quercetin and resveratrol supplementation in high fat diet fed mice.

Dietary quercetin and resveratrol have been frequently used in treating various diseases, but the underlying mechanisms are not entirely clear. Here, we report combined transcriptomic and metabonomic profiling that showed that the combined supplementation with quercetin and resveratrol produced synergistic effects on a high-fat diet-induced metabolic phenotype in mice. Histological and phenotypic improvements in serum and hepatic total cholesterol, insulin, fasting blood glucose, and HbA1c were also observed in mice receiving combined quercetin and resveratrol supplementation. This combined quercetin and resveratrol supplementation resulted in significant restoration of gene sets in functional pathways of glucose/lipid metabolism, liver function, cardiovascular system, and inflammation/immunity, which were altered by high fat diet feeding. The integration of transcriptomic and metabonomic data indicated quercetin and resveratrol supplementation enhanced processes of glycolysis and fatty acid oxidation, as well as suppressed gluconeogenesis. These alterations discovered at both the transcriptional and metabolic levels highlight the significance of combined "omics" platforms for elucidating mechanistic pathways altered by dietary polyphenols, such as quercetin and resveratrol, in a synergistic manner.

[Study on effects of baicalin, berberine and Astragalus polysaccharides and their combinative effects on aldose reductase in vitro].

OBJECTIVE: To observe the activities of baicalin, berberine and Astragalus polysaccharides and their combinative effects on aldose reductase (AR) by a screening model of aldose reductase inhibitor (ARI) in vitro. METHODS: The inhibition of AR by baicalin, berberine and Astragalus polysaccharides and positive drug (Epalrestat) in different concentrations were evaluated, and their combinative effects were studied according to orthogonal t design. RESULTS: Baicalin and berberine had remarkable inhibitory effects on AR, the inhibitory rates were (88.4 +/- 7.4)% and (69.0 +/- 9.4)% at the concentration of 300 microg/mL. However, the combinative effect of the inhibition on AR by the two compounds was antagonistic action. Astragalus polysaccharides had no activity of inhibition on AR. CONCLUSION: Baicalin and berberine are the potential AR inhibitors as they can inhibit the activity of AR in vitro.