A high-efficiency strategy integrating offline two-dimensional separation and data post-processing with dereplication: Characterization of bufadienolides in Venenum Bufonis as a case study

A powerful two-dimensional chromatography method for the non-target analysis of depolymerised lignin

BACKGROUND

Lignin is an abundant natural polymer obtained as a by-product from the fractionation of lignocellulosic biomass. In the name of a circular economy, lignin should be valorised into valuable chemicals or biomaterials and utilised instead of petrochemicals. For the development of efficient valorisation processes, the structural characterisation of lignin can be highly beneficial. However, this is an arduous task, as the isolated (and sometimes processed) lignin mainly consists of various neutral monomers but also oligomers. In addition, the material contains isomers, which can be especially problematic to separate and identify.

RESULTS

We present a powerful off-line comprehensive two-dimensional (2D) chromatography method combining liquid chromatography (LC), supercritical fluid chromatography (SFC), and high-resolution mass spectrometry for the non-target analysis of depolymerised lignin. The implementation of a 1-aminoanthracene column in the second dimension enabled a class separation of potential lignin monomers, dimers, trimers, and tetramers with an additional separation based on the number of hydroxyl groups and steric effects. The pentafluorophenyl column in the first dimension additionally improved the separation based on hydrophobicity. The comparison of off-line 2D LC × SFC to 1D SFC showed that besides the overall improved performance, the first method is also superior for the separation of isomers. Advanced data analysis methods (MS-DIAL, SIRIUS, and Feature-Based Molecular Network) were integrated into the non-target workflow to rapidly visualise and study the detected compounds, which proved to be especially beneficial for the characterisation of the separated isomers.

SIGNIFICANCE

The method yielded the first 2D LC plot demonstrating a classification of lignin compounds, which can be applied to compare various lignin sources and processing methods. In addition, the technique demonstrated improved separation of compounds, including isomers, which was especially beneficial as 77 % of the detected compounds had at least one isomer in the same lignin sample.

Identification of chemical constituents in pomegranate seeds based on ultra-high-performance supercritical fluid chromatography coupled with quadrupole time-of-flight mass spectrometry

Pomegranate seeds are a potential source of bioactive compounds. Nonetheless, most pomegranate seeds are discarded in the food processing industry, likely due to the lack of convincing data on their component analysis.

METHODS

To reveal the main chemical constituents of pomegranate seeds, a reliable and sensitive method based on ultra-high-performance supercritical fluid chromatography coupled with electrospray ionization and quadrupole time-of-flight mass spectrometry (MS) was developed. A time-dependent MSE data acquisition mode was applied to acquire the mass spectrometric data. The chemical constituents were identified by an automatic retrieval of a traditional Chinese medicine library and relevant literature.

RESULTS

A total number of 59 compounds, including fatty acids, sterols, vitamins, cerebrosides, phospholipids, flavonoids, phenylpropanoids, and others, were tentatively identified. Their possible fragmentation pathways and characteristic ions were proposed and elucidated.

CONCLUSIONS

The findings of this study, along with the developed methodology, could provide a reference for basic research on the pharmacodynamic substances of pomegranate seeds and shed light on their potential nutritional and therapeutic applications in the future.

A compounds annotation strategy using targeted molecular networking for offline two-dimensional liquid chromatography-mass spectrometry analysis: Yupingfeng as a case study

Component overlapping and long-time consumption hinder the data processing of offline two-dimensional liquid chromatography mass spectrometry (offline 2D-LC MS) system. Although molecular networking has been commonly employed in data processing of liquid chromatography mass spectrometry (LC-MS), its application in offline 2D-LC MS is challenged by voluminous and redundant data. In light of this, for the first time, a data deduplication and visualization strategy combining hand-in-hand alignment with targeted molecular networking (TMN) for compounds annotation of offline 2D-LC MS data was developed and applied to the chemical profile of Yupingfeng (YPF), a classical traditional Chinese medicine (TCM) prescription, as a case study. Firstly, an offline 2D-LC MS system was constructed for the separation and data acquisition of YPF extract. Then the data of 12 fractions derived from YPF were deconvoluted and aligned as a whole data file by hand-in-hand alignment, resulting in a 49.2% reduction in component overlapping (from 17951 to 9112 ions) and an improvement in the MS² spectrum quality of precursor ions. Subsequently, the MS²-similarity adjacency matrix of focused parent ions was computed by a self-building Python script, which realized the construction of an innovative TMN. Interestingly, the TMN was found to be able to efficiently distinguish and visualize the co-elution, in-source fragmentations and multi-type adduct ions in a clustering network. Consequently, a total of 497 compounds were successfully identified depending on only seven TMN analysis guided by product ions filtering (PIF) and neutral loss filtering (NLF) for the targeted compounds in YPF. This integrated strategy improved the efficiency of targeted compound discovery in offline 2D-LC MS data, also shown a huge scalability in accurate compound annotation of complex samples. In conclusion, our study developed available concepts and tools while providing a research paradigm for efficient and rapid compound annotation in complex samples such as TCM prescriptions, with YPF as an example.

On-line reversed-phase liquid chromatography x supercritical fluid chromatography coupled to high-resolution mass spectrometry: a powerful tool for the characterization of advanced biofuels

Bio-oils obtained by thermochemical or biochemical conversion of biomass represent a promising source of energy to complement fossil fuels, in particular for maritime or air transport for which the use of hydrogen or electricity appears complicated. As these bio-oils are very rich in water and heteroatoms, additional treatments are necessary before they can be used as biofuel. In order to improve the efficiency of these treatments, it is important to have a thorough knowledge of the composition of the bio-oil. The characterization of bio-oils is difficult because they are very complex mixtures with thousands of compounds covering a very wide range of molecular weight and polarity. Due to the high degree of orthogonality between the two chromatographic dimensions, the on-line combination of reversed-phase liquid chromatography and supercritical fluid chromatography (on-line RPLC x SFC) can significantly improve the characterization of such complex matrices. The hyphenation was optimized by selecting, in SFC, the stationary phase, the co-solvent, the make-up solvent prior to high resolution mass spectrometry (HRMS) and the injection solvent. Additionally, a new interface configuration is described. Quality descriptors such as the occupation of the separation space, the peak shapes and the signal intensity were considered to determine the optimal conditions. The best results were obtained with bare silica, a co-solvent composed of acetonitrile and methanol (50/50, v/v), a make-up solvent composed of methanol (90%) and water (10%) with formic acid (0.1%), an addition of co-solvent through an additional pump for SFC separation in a 2.1 mm column, and an hydro-organic solvent as injection solvent. The optimized setup was used to analyze two microalgae bio-oils: the full bio-oil coming from hydrothermal liquefaction and Soxhlet extraction of microalgae, and the gasoline cut obtained after distillation of the full bio-oil. Results in on-line RPLC x SFC-qTOF were particularly interesting, with very good peak shapes and high reproducibility. Moreover, the high degree of orthogonality for microalgae bio-oils of RPLC and SFC was highlighted by the very large occupation of the separation space. Isomeric profiles of compound families could be obtained in RPLC x SFC-qTOF and many isomers not separated in SFC alone were separated in RPLC and vice versa, thus showing the complementarity of the two chromatographic techniques.

Enhanced profiling and quantification of ginsenosides from mountain-cultivated ginseng and comparison with garden-cultivated ginseng

Panax ginseng can be generally divided into mountain-cultivated ginseng (MCG) and garden-cultivated ginseng (GCG). The market price of MCG is significantly higher than that of GCG. However, the chemical compositions of MCG and the differences from GCG remained unclear. In this study, an integrated strategy combing an offline two-dimensional liquid chromatography separation, LTQ-orbitrap dual mode acquisition, and Q-trap full quantification/quasi-quantification was proposed to explore and compare the chemical compositions of MCG. Consequently, 559 ginsenosides were characterized, among which 437 ginsenosides were in-depth characterized with α-chain and β-chain annotated. Subsequently, enhanced quantification of 213 ginsenosides was conducted in 57 batches of MCG and GCG. Ginsenosides were found more abundant in MCG than GCG. In addition, 25-year-old MCG could be distinctly differentiated from 15/20-year-old MCG. This strategy facilitated the enhanced profiling and comparison of ginsenosides, improved the quality control tactics of MCG and provided a reference approach for other ginseng related products.

Off-line two-dimensional separation involving supercritical fluid chromatography for the characterization of the wastewater from algae hydrothermal liquefaction

An off-line multidimensional method involving liquid chromatography combined with supercritical fluid chromatography was developed for the characterization of the wastewater of hydrothermal liquefaction of microalgae Chlorella sorokiniana. The first dimension consisted of a phenyl hexyl column operated in reversed-phase mode, whereas the second dimension was performed on a diol stationary phase. Optimization of the kinetic parameters of the first and second dimensions were performed, taking into account the fraction collection system. The beneficial effect of working at high flow rate in both dimensions, as well as the need to work with short columns (50 mm) in the second dimension was evidenced. Injection volume was also optimized in both dimensions. The first dimension benefited from on-column focusing, while in the second dimension, untreated water-rich fractions could be injected without peak deformation. The performances of offline LCxSFC were compared to LC-HRMS, SFC-HRMS and LCxLC-HRMS for the analysis of the wastewater. Despite a long analysis time of 3.3h, the off-line separation coupled to high-resolution mass spectrometry exhibited a very large orthogonality with 75 % occupation rate of the separation space, reaching an effective peak capacity of 1050. While other evaluated techniques were faster, one-dimensional techniques failed to separate the numerous isomers while LCxLC exhibited lower orthogonality (45% occupation rate).

Progress and prediction of multicomponent quantification in complex systems with practical LC-UV methods

Complex systems exist widely, including medicines from natural products, functional foods, and biological samples. The biological activity of complex systems is often the result of the synergistic effect of multiple components. In the quality evaluation of complex samples, multicomponent quantitative analysis (MCQA) is usually needed. To overcome the difficulty in obtaining standard products, scholars have proposed achieving MCQA through the "single standard to determine multiple components (SSDMC)" approach. This method has been used in the determination of multicomponent content in natural source drugs and the analysis of impurities in chemical drugs and has been included in the Chinese Pharmacopoeia. Depending on a convenient (ultra) high-performance liquid chromatography method, how can the repeatability and robustness of the MCQA method be improved? How can the chromatography conditions be optimized to improve the number of quantitative components? How can computer software technology be introduced to improve the efficiency of multicomponent analysis (MCA)? These are the key problems that remain to be solved in practical MCQA. First, this review article summarizes the calculation methods of relative correction factors in the SSDMC approach in the past five years, as well as the method robustness and accuracy evaluation. Second, it also summarizes methods to improve peak capacity and quantitative accuracy in MCA, including column selection and two-dimensional chromatographic analysis technology. Finally, computer software technologies for predicting chromatographic conditions and analytical parameters are introduced, which provides an idea for intelligent method development in MCA. This paper aims to provide methodological ideas for the improvement of complex system analysis, especially MCQA.

Combining multidimensional chromatography-mass spectrometry and feature-based molecular networking methods for the systematic characterization of compounds in the supercritical fluid extract of Tripterygium wilfordii Hook F

Tripterygium wilfordii Hook F from the family Celastraceae is a traditional Chinese medicine (TCM) whose principal chemical constituents are terpenoids, including sesquiterpene alkaloids and diterpenoids, which have unique and diverse structures and remarkable biological activities. In order to advance pharmacological research and guide the preparation of monomer compounds derived from T. wilfordii, a systematic approach to efficiently discover new compounds or their derivatives is needed. Herein, compound separation and identification were performed by offline reversed-phase × supercritical fluid chromatography coupled mass spectrometry (RP × SFC-Q-TOF-MS/MS) and Global Natural Product Social (GNPS) molecular networking. The 2D chromatography system exhibited a high degree of orthogonality and significant peak capacity, and SFC has an advantage during the separation of sesquiterpene alkaloid isomers. Feature-based molecular networking offers the great advantage of quickly detecting and clustering unknown compounds, which greatly assists in intuitively judging the type of compound, and this networking technique has the potential to dramatically accelerate the identification and characterization of compounds from natural sources. A total of 324 compounds were identified and quantitated, including 284 alkaloids, 22 diterpenoids and 18 triterpenoids, which means that there are numerous potential new compounds with novel structures to be further explored. Overall, feature-based molecular networking provides an effective method for discovering and characterizing novel compounds and guides the separation and preparation of targeted natural products.

Rapid Profiling of Metabolites Combined with Network Pharmacology to Explore the Potential Mechanism of Sanguisorba officinalis L. against Thrombocytopenia

Sanguisorba officinalis L. (SO), a well-known herbal medicine, has been proven to show effect against thrombocytopenia. However, metabolites of SO in vivo are still unclear, and the underlying mechanism of SO against thrombocytopenia from the aspect of metabolites have not been well elucidated. In this study, an improved analytical method combined with UHPLC-QTOF MS and a molecular network was developed for the rapid characterization of metabolites in vivo based on fragmentation patterns. Then, network pharmacology (NP) was used to elucidate the potential mechanism of SO against thrombocytopenia. As a result, a total of 1678 exogenous metabolites were detected in urine, feces, plasma, and bone marrow, in which 104 metabolites were tentatively characterized. These characterized metabolites that originated from plasma, urine, and feces were then imported to the NP analysis. The results showed that the metabolites from plasma, urine, and feces could be responsible for the pharmacological activity against thrombocytopenia by regulating the PI3K-Akt, MAPK, JAK-STAT, VEGF, chemokine, actin cytoskeleton, HIF-1, and pluripotency of stem cells. This study provides a rapid method for metabolite characterization and a new perspective of underlying mechanism study from the aspect of active metabolites in vivo.

Advanced Development of Supercritical Fluid Chromatography in Herbal Medicine Analysis

The greatest challenge in the analysis of herbal components lies in their variety and complexity. Therefore, efficient analytical tools for the separation and qualitative and quantitative analysis of multi-components are essential. In recent years, various emerging analytical techniques have offered significant support for complicated component analysis, with breakthroughs in selectivity, sensitivity, and rapid analysis. Among these techniques, supercritical fluid chromatography (SFC) has attracted much attention because of its high column efficiency and environmental protection. SFC can be used to analyze a wide range of compounds, including non-polar and polar compounds, making it a prominent analytical platform. The applicability of SFC for the separation and determination of natural products in herbal medicines is overviewed in this article. The range of applications was expanded through the selection and optimization of stationary phases and mobile phases. We also focus on the two-dimensional SFC analysis. This paper provides new insight into SFC method development for herbal medicine analysis.

The combination of UHPLC-HRMS and molecular networking improving discovery efficiency of chemical components in Chinese Classical Formula

Background

It is essential to identify the chemical components for the quality control methods establishment of Chinese Classical Formula (CCF). However, CCF are complex mixture of several herbal medicines with huge number of different compounds and they are not equal to the combination of chemical components from each herb due to particular formula ratio and preparation techniques. Therefore, it is time-consuming to identify compounds in a CCF by analyzing the LC–MS/MS data one by one, especially for unknown components.

Methods

An ultra-high pressure liquid chromatography-linear ion trap-orbitrap high resolution mass spectrometry (UHPLC-LTQ-Orbitrap-MS/MS) approach was developed to comprehensively profile and characterize multi-components in CCF with Erdong decoction composed of eight herbal medicines as an example. Then the MS data of Erdong decoction was analyzed by MS/MS-based molecular networking and these compounds with similar structures were connected to each other into a cluster in the network map. Then the unknown compounds connected to known compounds in a cluster of the network map were identified due to their similar structures.

Results

Based on the clusters of the molecular networking, 113 compounds were rapidly tentative identification from Erdong decoction for the first time in the negative mode, which including steroidal saponins, triterpenoid saponins, flavonoid O-glycosides and flavonoid C-glycosides. In addition, 10 alkaloids were tentatively identified in the positive mode from Nelumbinis folium by comparison with literatures.

Conclusion

MS/MS-based molecular networking technique is very useful for the rapid identification of components in CCF. In Erdong decoction, this method was very suitable for the identification of major steroidal saponins, triterpenoid saponins, and flavonoid C-glycosides.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13020-021-00459-6.

Insight into chemical basis of traditional Chinese medicine based on the state-of-the-art techniques of liquid chromatography-mass spectrometry

Traditional Chinese medicine (TCM) has been an indispensable source of drugs for curing various human diseases. However, the inherent chemical diversity and complexity of TCM restricted the safety and efficacy of its usage. Over the past few decades, the combination of liquid chromatography with mass spectrometry has contributed greatly to the TCM qualitative analysis. And novel approaches have been continuously introduced to improve the analytical performance, including both the data acquisition methods to generate a large and informative dataset, and the data post-processing tools to extract the structure-related MS information. Furthermore, the fast-developing computer techniques and big data analytics have markedly enriched the data processing tools, bringing benefits of high efficiency and accuracy. To provide an up-to-date review of the latest techniques on the TCM qualitative analysis, multiple data-independent acquisition methods and data-dependent acquisition methods (precursor ion list, dynamic exclusion, mass tag, precursor ion scan, neutral loss scan, and multiple reaction monitoring) and post-processing techniques (mass defect filtering, diagnostic ion filtering, neutral loss filtering, mass spectral trees similarity filter, molecular networking, statistical analysis, database matching, etc.) were summarized and categorized. Applications of each technique and integrated analytical strategies were highlighted, discussion and future perspectives were proposed as well.

An enhanced strategy integrating offline superimposed two-dimensional separation with mass defect filter and diagnostic ion filter: Comprehensive characterization of steroid alkaloids in Fritillariae Pallidiflorae Bulbus as a case study

The inherent complexity of traditional Chinese medicines necessitates the application of multi-dimensional information to accomplish comprehensive profiling and confirmative identification of their chemical components. In this study, we display an enhanced strategy by integrating offline superimposed two-dimensional separation (S-2D-LC) with mass defect filter and diagnostic ion filter to comprehensively characterize the alkaloid composition of Fritillariae Pallidiflorae Bulbus (FPB). The superimposed HILIC × RP and UPCC × RP offline two-dimensional liquid chromatography system was constructed with superior orthogonality (R²=0.004 and R²=0.001) for chromatographic separation. In total, 70 fractions were collected after the first-dimensional chromatographic separation (HILIC and UPCC) and then analyzed by the second-dimensional reversed phase (RP) liquid chromatography coupled with Q-TOF/MS/MS in FAST DDA acquisition mode. A four-step interpretation strategy combining mass defect filter with diagnostic ion filter was developed to rapidly characterize alkaloids in Fritillaria species. Ultimately, a sum of 529 Fritillaria alkaloids were characterized from two botanical origins of FPB. The integrated strategy is practical to efficiently expose and comprehensively characterize more trace and isomeric components in complex herbal medicines.

"Force iteration molecular designing" strategy for the systematic characterization and discovery of new protostane triterpenoids from Alisma Rhizoma by UHPLC/LTQ-Orbitrap-MS

Comprehensive analysis and identification of chemical components are of great significance for evaluating the efficacy and safety of herbal medicines, as well as for drug exploitation and development. Here we developed a "force iteration molecular designing" strategy, by combing a database-based in-house software for a precursor ion list (PIL) and PIL-triggered collision-induced dissociation-MS² and high-energy C-trap dissociation-MS² (PIL-CID/MS²-HCD/MS²) on an LTQ-Orbitrap mass spectrometer, aiming for the systematic characterization and discovery of new protostane triterpenoids (PTs) from Alisma Rhizoma (AR). AR was a well-known herbal remedy widely used for diarrhea, but its systematic characterization and comparison between two botanical origins have not been reported. Firstly, in-house software was developed based on force iteration, to generate a PIL that contains 483 accurate precursor ions. Secondly, to facilitate the acquisition of rich fragments and diagnostic ions sufficient for the structural elucidation of different types of PTs, a hybrid data acquisition method, namely PIL-CID/MS²-HCD/MS², was generated. Thirdly, a total of 473 PTs were rapidly characterized from two botanical origins of AR according to an established four-step interpretation method, and the common constituents were 277 with ratio 70% (277/395) and 78% (277/355) in the rhizome of Alisma plantago-aquatica and A. orientale, respectively. Finally, two new PTs were isolated and unambiguously identified by NMR verifying the feasibility of this combined data acquisition strategy. This integrated strategy could improve the efficiency in the detection of new compounds in a single run and is practical to comprehensively characterize the complex components in herbal medicines.

An integrated strategy for comprehensive characterization of metabolites and metabolic profiles of bufadienolides from Venenum Bufonis in rats

Comprehensive characterization of metabolites and metabolic profiles in plasma has considerable significance in determining the efficacy and safety of traditional Chinese medicine (TCM) in vivo. However, this process is usually hindered by the insufficient characteristic fragments of metabolites, ubiquitous matrix interference, and complicated screening and identification procedures for metabolites. In this study, an effective strategy was established to systematically characterize the metabolites, deduce the metabolic pathways, and describe the metabolic profiles of bufadienolides isolated from Venenum Bufonis in vivo. The strategy was divided into five steps. First, the blank and test plasma samples were injected into an ultra-high performance liquid chromatography/linear trap quadrupole-orbitrap-mass spectrometry (MS) system in the full scan mode continuously five times to screen for valid matrix compounds and metabolites. Second, an extension-mass defect filter model was established to obtain the targeted precursor ions of the list of bufadienolide metabolites, which reduced approximately 39% of the interfering ions. Third, an acquisition model was developed and used to trigger more tandem MS (MS/MS) fragments of precursor ions based on the targeted ion list. The acquisition mode enhanced the acquisition capability by approximately four times than that of the regular data-dependent acquisition mode. Fourth, the acquired data were imported into Compound Discoverer software for identification of metabolites with metabolic network prediction. The main in vivo metabolic pathways of bufadienolides were elucidated. A total of 147 metabolites were characterized, and the main biotransformation reactions of bufadienolides were hydroxylation, dihydroxylation, and isomerization. Finally, the main prototype bufadienolides in plasma at different time points were determined using LC-MS/MS, and the metabolic profiles were clearly identified. This strategy could be widely used to elucidate the metabolic profiles of TCM preparations or Chinese patent medicines in vivo and provide critical data for rational drug use.

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Extension-mass defect filter model could reduce about 39% interfering ions.

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The optimized acquisition mode enhanced about 4 times acquisition capability than regular DDA mode.

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147 metabolites were characterized with metabolic network prediction, and the metabolic pathways were deduced in plasmas.

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The quantitative method of 14 prototypes was established by LC-MS/MS for metabolic profiles study.