Metabolomics data fusion between near infrared spectroscopy and high-resolution mass spectrometry: A synergetic approach to boost performance or induce confusion

Multi-Omics Approaches for Freshness Estimation and Detection of Illicit Conservation Treatments in Sea Bass (Dicentrarchus Labrax): Data Fusion Applications

Fish freshness consists of complex endogenous and exogenous processes; therefore, the use of a few parameters to unravel illicit practices could be insufficient. Moreover, the development of strategies for the identification of such practices based on additives known to prevent and/or delay fish spoilage is still limited. The paper deals with the identification of the effect played by a Cafodos solution on the conservation state of sea bass at both short-term (3 h) and long-term (24 h). Controls and treated samples were characterized by a multi-omic approach involving proteomics, lipidomics, metabolomics, and metagenomics. Different parts of the fish samples were studied (muscle, skin, eye, and gills) and sampled through a non-invasive procedure based on EVA strips functionalized by ionic exchange resins. Data fusion methods were then applied to build models able to discriminate between controls and treated samples and identify the possible markers of the applied treatment. The approach was effective in the identification of the effect played by Cafodos that proved to be different in the short- and long-term and complex, involving proteins, lipids, and small molecules to a different extent.

Application of Data Fusion in Traditional Chinese Medicine: A Review

Traditional Chinese medicine is characterized by numerous chemical constituents, complex components, and unpredictable interactions among constituents. Therefore, a single analytical technique is usually unable to obtain comprehensive chemical information. Data fusion is an information processing technology that can improve the accuracy of test results by fusing data from multiple devices, which has a broad application prospect by utilizing chemometrics methods, adopting low-level, mid-level, and high-level data fusion techniques, and establishing final classification or prediction models. This paper summarizes the current status of the application of data fusion strategies based on spectroscopy, mass spectrometry, chromatography, and sensor technologies in traditional Chinese medicine (TCM) in light of the latest research progress of data fusion technology at home and abroad. It also gives an outlook on the development of data fusion technology in TCM analysis to provide references for the research and development of TCM.

Augmented region of interest for untargeted metabolomics mass spectrometry (AriumMS) of multi-platform-based CE-MS and LC-MS data

In mass spectrometry (MS)-based metabolomics, there is a great need to combine different analytical separation techniques to cover metabolites of different polarities and apply appropriate multi-platform data processing. Here, we introduce AriumMS (augmented region of interest for untargeted metabolomics mass spectrometry) as a reliable toolbox for multi-platform metabolomics. AriumMS offers augmented data analysis of several separation techniques utilizing a region-of-interest algorithm. To demonstrate the capabilities of AriumMS, five datasets were combined. This includes three newly developed capillary electrophoresis (CE)-Orbitrap MS methods using the recently introduced nanoCEasy CE-MS interface and two hydrophilic interaction liquid chromatography (HILIC)-Orbitrap MS methods. AriumMS provides a novel mid-level data fusion approach for multi-platform data analysis to simplify and speed up multi-platform data processing and evaluation. The key feature of AriumMS lies in the optimized data processing strategy, including parallel processing of datasets and flexible parameterization for processing of individual separation methods with different peak characteristics. As a case study, Saccharomyces cerevisiae (yeast) was treated with a growth inhibitor, and AriumMS successfully differentiated the metabolome based on the augmented multi-platform CE-MS and HILIC-MS investigation. As a result, AriumMS is proposed as a powerful tool to improve the accuracy and selectivity of metabolome analysis through the integration of several HILIC-MS/CE-MS techniques.

Development of a variety and quality evaluation method for Amomi fructus using GC, electronic tongue, and electronic nose

Amomi fructus is rich in volatile components and valuable as a medicine and edible spice. However, the quality of commercially available A. fructus varies, and issues with mixed sources and adulteration by similar products are common. In addition, due to incomplete identification methods, rapid detection of the purchased A. fructus quality is still an issue. In this study, we developed qualitative and quantitative evaluation models to assess the variety and quality of A. fructus using GC, electronic tongue, and electronic nose to provide a rapid and accurate variety and quality evaluation method of A. fructus. The models performed well; the qualitative authenticity model had an accuracy of 1.00 (n = 64), the accuracy of the qualitative origin model was 0.86 (n = 44), and the quantitative model was optimal on the sensory fusion data from the electronic tongue and electronic nose combined with borneol acetate content, with R ² = 0.7944, RMSEF = 0.1050, and RMSEP = 0.1349. The electronic tongue and electronic nose combined with GC quickly and accurately evaluated the variety and quality of A. fructus, and the introduction of multi-source information fusion technology improved the model prediction accuracy. This study provides a useful tool for quality evaluation of medicine and food.

A Synergetic Strategy for Brand Characterization of Colla Corii Asini (Ejiao) by LIBS and NIR Combined with Partial Least Squares Discriminant Analysis

A synergetic strategy was proposed to address the critical issue in the brand characterization of Colla corii asini (Ejiao, CCA), a precious traditional Chinese medicine (TCM). In all brands of CCA, Dong'e Ejiao (DEEJ) is an intangible cultural heritage resource. Seventy-eight CCA samples (including forty DEEJ samples and thirty-eight samples from other different manufacturers) were detected by laser-induced breakdown spectroscopy (LIBS) and near-infrared spectroscopy (NIR). Partial least squares discriminant analysis (PLS-DA) models were built first considering individual techniques separately, and then fusing LIBS and NIR data at low-level. The statistical parameters including classification accuracy, sensitivity, and specificity were calculated to evaluate the PLS-DA model performance. The results demonstrated that two individual techniques show good classification performance, especially the NIR. The PLS-DA model with single NIR spectra pretreated by the multiplicative scatter correction (MSC) method was preferred as excellent discrimination. Though individual spectroscopic data obtained good classification performance. A data fusion strategy was also attempted to merge atomic and molecular information of CCA. Compared to a single data block, data fusion models with SNV and MSC pretreatment exhibited good predictive power with no misclassification. This study may provide a novel perspective to employ a comprehensive analytical approach to brand discrimination of CCA. The synergetic strategy based on LIBS together with NIR offers atomic and molecular information of CCA, which could be exemplary for future research on the rapid discrimination of TCM.

Comparison of Ophiopogon japonicus and Liriope spicata var. prolifera from Different Origins Based on Multi-Component Quantification and Anticancer Activity

The tuberous root of Ophiopogon japonicus (Thunb.) Ker-Gawl. is a well-known Chinese medicine also called Maidong (MD) in Chinese. It could be divided into "Chuanmaidong" (CMD) and "Zhemaidong" (ZMD), according to the geographic origins. Meanwhile, the root of Liriope spicata (Thunb.) Lour. var. prolifera Y. T. Ma (SMD) is occasionally used as a substitute for MD in the market. In this study, a reliable pressurized liquid extraction and HPLC-DAD-ELSD method was developed for the simultaneous determination of nine chemical components, including four steroidal saponins (ophiopojaponin C, ophiopogonin D, liriopesides B and ophiopogonin D'), four homoisoflavonoids (methylophiopogonone A, methylophiopogonone B, methylophiopogonanone A and methylophiopogonanone B) and one sapogenin (ruscogenin) in CMD, ZMD and SMD. The method was validated in terms of linearity, sensitivity, precision, repeatability and accuracy, and then applied to the real samples from different origins. The results indicated that there were significant differences in the contents of the investigated compounds in CMD, ZMD and SMD. Ruscogenin was not detected in all the samples, and liriopesides B was only found in SMD samples. CMD contained higher ophiopogonin D and ophiopogonin D', while the other compounds were more abundant in ZMD. Moreover, the anticancer effects of the herbal extracts and selected components against A2780 human ovarian cancer cells were also compared. CMD and ZMD showed similar cytotoxic effects, which were stronger than those of SMD. The effects of MD may be due to the significant anticancer potential of ophiopognin D' and homoisoflavonoids. These results suggested that there were great differences in the chemical composition and pharmacological activity among CMD, ZMD and SMD; thus, their origins should be carefully considered in clinical application.

Authenticity and species identification of Fritillariae cirrhosae: a data fusion method combining electronic nose, electronic tongue, electronic eye and near infrared spectroscopy

This paper focuses on determining the authenticity and identifying the species of Fritillariae cirrhosae using electronic nose, electronic tongue, and electronic eye sensors, near infrared and mid-level data fusion. 80 batches of Fritillariae cirrhosae and its counterfeits (including several batches of Fritillaria unibracteata Hsiao et K.C. Hsia, Fritillaria przewalskii Maxim, Fritillaria delavayi Franch and Fritillaria ussuriensis Maxim) were initially identified by Chinese medicine specialists and by criteria in the 2020 edition of Chinese Pharmacopoeia. After obtaining the information from several sensors we constructed single-source PLS-DA models for authenticity identification and single-source PCA-DA models for species identification. We selected variables of interest by VIP value and Wilk's lambda value, and we subsequently constructed the three-source fusion model of intelligent senses and the four-source fusion model of intelligent senses and near-infrared spectroscopy. We then explained and analyzed the four-source fusion models based on the sensitive substances detected by key sensors. The accuracies of single-source authenticity PLS-DA identification models based on electronic nose, electronic eye, electronic tongue sensors and near-infrared were respectively 96.25%, 91.25%, 97.50% and 97.50%. The accuracies of single-source PCA-DA species identification models were respectively 85%, 71.25%, 97.50% and 97.50%. After three-source data fusion, the accuracy of the authenticity identification of the PLS-DA identification model was 97.50% and the accuracy of the species identification of the PCA-DA model was 95%. After four-source data fusion, the accuracy of the authenticity of the PLS-DA identification model was 98.75% and the accuracy of the species identification of the PCA-DA model was 97.50%. In terms of authenticity identification, four-source data fusion can improve the performance of the model, while for the identification of the species the four-source data fusion failed to optimize the performance of the model. We conclude that electronic nose, electronic tongue, electronic eye data and near-infrared spectroscopy combined with data fusion and chemometrics methods can identify the authenticity and determine the species of Fritillariae cirrhosae. Our model explanation and analysis can help other researchers identify key quality factors for sample identification. This study aims to provide a reference method for the quality evaluation of Chinese herbs.

Data fusion of electronic noses and electronic tongues aids in botanical origin identification on imbalanced Codonopsis Radix samples

Codonopsis Radix (CR) is an edible food and traditional Chinese herb medicine in China. Various varieties of Codonopsis Radix have different tastes. To make the flavor of processed food stable, two kinds of electronic sensory devices, electronic nose and electronic tongue, were used to establish a discrimination model to identify the botanical origin of each sample. The optimal model built on the 88 batches of samples was selected from the models trained with all combination of two pretreatment methods and three classification methods. A comparison were performed on the models trained on the data collected by electronic nose and electronic tongue. The results showed that the model trained on the fused dataset outperformed the models trained separately on the electronic nose data and electronic tongue data. The two preprocessing approaches could improve the prediction performance of all classification methods. Classification and Regression Tree approach performed better than Partial Least Square Discriminant Analysis and Linear Discriminant Analysis in terms of accuracy. But Classification and Regression Tree tends to assign the samples of minority class to the majority class. Meanwhile, Partial Least Square Discriminant Analysis keeps a good balance between the identification requirements of all the two groups of samples. Taking all the results above, the model built using the Partial Least Square Discriminant Analysis method on the fused data after z-score was used to identify the botanical origin of Codonopsis Radix.

Application of Analytical Technologies in the Discrimination and Authentication of Herbs from Fritillaria: A Review

Medicinal plants of Fritillaria are widely distributed in numerous countries around the world and possess excellent antitussive and expectorant effects. In particular, Fritillariae Bulbus (FB) as a precious traditional medicine has thousands of years of medical history in China. Herbs of Fritillaria have a high market value and demand while limited by harsh growing circumstances and scarce wild resources. As a consequence, fraudulent behaviors are regularly engaged by the unscrupulous merchants in an attempt to reap greater profits. It is of an urgent need to evaluate the quality of Fritillaria herbs and their products using various analytical instruments and techniques. This review has scrutinized approximately 160 articles from 1995 to 2022 published on the investigation of Fritillaria herbs and related herbal products. The botanical classification of genus Fritillaria, types of counterfeits, technologies applied for differentiating Fritillaria species were comprehensively summarized and discussed in the current review. Molecular and chromatographic identification were the dominant technologies in the authentication of Fritillaria herbs. Additionally, we brought some potential and promising technologies and analytical strategies into attention, which are worthy attempting in the future researches. This review could conduce to excellent reference value for further investigations of the authenticity assessment of Fritillaria species.

Data Fusion Approach to Simultaneously Evaluate the Degradation Process Caused by Ozone and Humidity on Modern Paint Materials

The knowledge of the atmospheric degradation reactions affecting the stability of modern materials is still of current interest. In fact, environmental parameters, such as relative humidity (RH), temperature, and pollutant agents, often fluctuate due to natural or anthropogenic climatic changes. This study focuses on evaluating analytical and statistical strategies to investigate the degradation processes of acrylic and styrene-acrylic paints after exposure to ozone (O3) and RH. A first comparison of FTIR and Py-GC/MS results allowed to obtain qualitative information on the degradation products and the influence of the pigments on the paints' stability. The combination of these results represents a significant potential for the use of data fusion methods. Specifically, the datasets obtained by FTIR and Py-GC/MS were combined using a low-level data fusion approach and subsequently processed by principal component analysis (PCA). It allowed to evaluate the different chemical impact of the variables for the characterization of unaged and aged samples, understanding which paint is more prone to ozone degradation, and which aging variables most compromise their stability. The advantage of this method consists in simultaneously evaluating all the FTIR and Py-GC/MS variables and describing common degradation patterns. From these combined results, specific information was obtained for further suitable conservation practices for modern and contemporary painted films.

A gradient-based discriminant analysis method for process quality control of carbonized TCM via Fourier transform near infrared spectroscopy: A case study on carbonized Typhae Pollen

Carbonized traditional Chinese medicine (TCM) is a kind of distinctive traditional drug which has been widely used in various bleeding syndromes for over two thousand years, and most of them are still in clinical use. Although they share similar processing method: stir-frying, there are no specific quality standards and few quality control researches carried out on carbonized TCM up until now. Carbonized Typhae Pollen (CTP) is a typical carbonized TCM with efficacy of eliminating blood stasis and stanching bleeding. In this study, a novel process quality control model coupled with near infrared spectroscopy was established, called Gradient-based Discriminant Analysis method (GDA). Compared with conventional modeling methods (Convolutional Neural Network, Linear Discriminant Analysis, Standard Normal Variate-LDA), GDA model applied in fiber optic probe acquisition mode exhibited highest test accuracy (0.961), satisfactory correct identification (internal validation, 100%; external validation, 97.1%) and excellent model stability. This method provided a perfect guideline for process quality control of Carbonized TCM as well as ensured their clinical efficacy.

A Practical Protocol for a Comprehensive Evaluation of Sulfur Fumigation of Trichosanthis Radix Based on Both Non-Targeted and Widely Targeted Metabolomics

Trichosanthis Radix (TR) is one of the most severely sulfur-fumigated herbs in the market, whose transformation mechanism of chemical compositions and sulfur-fumigation markers of TR have not been clarified. To excavate characteristic sulfur-fumigation markers of TR samples, this study brings up a practical protocol using both ultra-performance liquid chromatography/quadrupole time-of-flight-mass spectrum (UPLC-ESI-QTOF-MS/MS)-based non-targeted metabolomics and ultra-performance liquid chromatography/electrospray ionization/quadrupole multiple-stage linear ion-trap mass spectrum (UPLC-ESI-QTRAP-MS/MS)-based widely targeted metabolomics. The results of study demonstrated that five characteristic markers are sulfur-containing components, which were identified as p-Hydroxybenzyl hydrogen sulfite, cucurbitacin D sulfite I, cucurbitacin D sulfite II, cucurbitacin B sulfite I, and cucurbitacin B sulfite II, respectively. Additionally, cucurbitacin B and D were also filtered and identified as the characteristic sulfur-fumigation markers. Meanwhile, the different sulfur-fumigation extent of TR samples was tested by chemical transformations analysis and sulfur dioxide residues test. Further, 58.16% (139 of 239) of the differential metabolites content significantly reduced in sulfur-fumigated TR samples. Besides, 20 kinds of non-sulfur marker metabolites were tested to evaluate the quality of TR samples before and after sulfur fumigation, predominantly including phenolic acids, amino acids, lipids and nucleotides. Taking TR as an example, this work provides a comprehensive practical protocol for the quality supervision of sulfur-fumigation herbs.

A rapid analysis method of safflower (Carthamus tinctorius L.) using combination of computer vision and near-infrared

The quality of safflower (Carthamus tinctorius L.) in the market is uneven due to the problems of dyeing and adulteration of safflower, and there is no perfect standard for the classification of quality grade of safflower at present. In this study, computer vision (CV) and near-infrared (NIR) were combined to realize the rapid and nondestructive analysis of safflower. First, the partial least squares discrimination analysis (PLS-DA) model was used to qualitatively identify the dyed safflower from 150 samples. Then the partial least squares (PLS) model was used for quantitative analysis of the hydroxy safflower yellow pigment A (HSYA) and water extract of undyed safflower. Herein, the discrimination rate of PLS-DA model reached 100%, and the residual predictive deviation (RPD) values of the PLS models for HSYA and water extract were 2.5046 and 5.6195, respectively. It indicated that the rapid analysis method combining CV and NIR was reliable, and its results can provide important reference for the formulation of safflower quality classification standards in the market.

Metabolomic tools used in marine natural product drug discovery

Introduction: The marine environment is a very promising resource for natural product research, with many of these reaching the market as new drugs, especially in the field of cancer therapy as well as the drug discovery pipeline for new antimicrobials. Exploitation for bioactive marine compounds with unique structures and novel bioactivity such as the isoquinoline alkaloid; trabectedin, the polyether macrolide; halichondrin B, and the peptide; dolastatin 10, requires the use of analytical techniques, which can generate unbiased, quantitative, and qualitative data to benefit the biodiscovery process. Metabolomics has shown to bridge this understanding and facilitate the development of new potential drugs from marine sources and particularly their microbial symbionts.Areas covered: In this review, articles on applied secondary metabolomics ranging from 1990-2018 as well as to the last quarter of 2019 were probed to investigate the impact of metabolomics on drug discovery for new antibiotics and cancer treatment.Expert opinion: The current literature review highlighted the effectiveness of metabolomics in the study of targeting biologically active secondary metabolites from marine sources for optimized discovery of potential new natural products to be made accessible to a R&D pipeline.

A proposed protocol based on integrative metabonomics analysis for the rapid detection and mechanistic understanding of sulfur fumigation of Chinese herbal medicines

In the current work, Lonicera japonica Flos (FLJ) was selected as a model Chinese herbal medicine (CHM) and a protocol was proposed for the rapid detection of sulfur-fumigated (SF) CHMs. A multiple metabonomics analysis was conducted using HPLC, NIR spectroscopy and a UHPLC-LTQ-Orbitrap mass spectrometer. First, the group discriminatory potential of each technique was respectively investigated based on PCA. Then, the effect of mid-level metabonomics data fusion on sample spatial distribution was evaluated based on data obtained using the above three technologies. Furthermore, based on the acquired HRMS data, 76 markers discriminating SF from non-sulfur-fumigated (NSF) CHMs were observed and 49 of them were eventually characterized. Moreover, NIR absorptions of 18 sulfur-containing markers were identified to be in close correlation with the discriminatory NIR wavebands. In conclusion, the proposed protocol based on integrative metabonomics analysis that we established for the rapid detection and mechanistic explanation of the sulfur fumigation of CHMs was able to achieve variable selection, enhance group separation and reveal the intrinsic mechanism of the sulfur fumigation of CHMs.

Drug Metabolite Cluster-Based Data-Mining Method for Comprehensive Metabolism Study of 5-hydroxy-6,7,3',4'-tetramethoxyflavone in Rats

The screening of drug metabolites in biological matrixes and structural characterization based on product ion spectra is among the most important, but also the most challenging due to the significant interferences from endogenous species. Traditionally, metabolite detection is accomplished primarily on the basis of predicted molecular masses or fragmentation patterns of prototype drug metabolites using ultra-high performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS). Although classical techniques are well-suited for achieving the partial characterization of prototype drug metabolites, there is a pressing need for a strategy to enable comprehensive drug metabolism depiction. Therefore, we present drug metabolite clusters (DMCs), different from, but complementary to, traditional approaches for mining the information regarding drugs and their metabolites on the basis of raw, processed, or identified tandem mass spectrometry (MS/MS) data. In this paper, we describe a DMC-based data-mining method for the metabolite identification of 5-hydroxy-6,7,3′,4′-tetramethoxyflavone (HTF), a typical hydroxylated-polymethoxyflavonoid (OH-PMF), which addressed the challenge of creating a thorough metabolic profile. Consequently, eight primary metabolism clusters, sixteen secondary metabolism clusters, and five tertiary metabolism clusters were proposed and 106 metabolites (19 potential metabolites included) were detected and identified positively and tentatively. These metabolites were presumed to generate through oxidation (mono-oxidation, di-oxidation), methylation, demethylation, methoxylation, glucuronidation, sulfation, ring cleavage, and their composite reactions. In conclusion, our study expounded drug metabolites in rats and provided a reference for further research on therapeutic material basis and the mechanism of drugs.

Traceability the provenience of cultivated Paris polyphylla Smith var. yunnanensis using ATR-FTIR spectroscopy combined with chemometrics

The conventional procedures, based on attenuated total reflectance-Fourier transform infrared spectrometry (ATR-FTIR), have been developed for the origins traceability of cultivated Paris polyphylla Smith var. yunnanensis (PPY) samples with the help of partial least square discriminant analysis (PLS-DA) and random forest. In this study, a set of 219 batch cultivated PPY samples, containing the cultivation years of 5, 6 and 7, and covering the municipal districts of Chuxiong, Dali, Honghe, Lijiang and Yuxi in Yunnan Province, China, were used to build the discrimination models. Firstly, a visualized analysis was carried out by t-distributed stochastic neighbor embedding (t-SNE) to reduce each data point in a two-dimensional map and make a knowledge of the sample distribution tendency. Secondly, the single spectra data sets of Paridis rhizome and leaf tissues, and the combination of these two data sets with variable selection (mid-level data fusion strategy), were used to establish PLS-DA and random forest models, and parallelly compared the model performance. Results demonstrated that the discrimination ability of PLS-DA preceded the random forest model, and the classification performance was remarkably improved after mid-level data fusion. These results verified each other by 5-, 6- and 7-year old Paridis samples and indicated that the model performance established in the present study was reliable. Besides, five agronomic characters, including the plant height, dry weight of rhizome and leaf tissues, and the allocation of rhizome and leaf were determined and analyzed, results of which indicated that the dry weight and their allocation was significantly different among various origins and fluctuated with the cultivation years. This study was using a comprehensive and green analytical method to discriminate the cultivated Paridis according to their provenances, which was simultaneously benefited for the appropriate cultivation areas selection based on the dry weight of rhizome tissues.