Two-dimensional Reversed-phase Liquid Chromatography Research Articles

Innovative orthogonal two-dimensional reversed-phase liquid chromatography × supercritical fluid chromatography with a phenyl/tetrazole stationary phase for the preparative isolation of diarylheptanoids

In this investigation, we successfully isolated and purified natural diarylheptanoids using an orthogonal offline two-dimensional RPLC × SFC approach, employing only the phenyl/tetrazole stationary phase. First, a styrene-divinylbenzene matrix medium pretreatment liquid chromatography system effectively processed chlorophyll-containing plant extract solution with a recovery rate of 33.8 %, obviating the need for concentration steps. Subsequently, an offline two-dimensional RPLC × SFC employing only the phenyl/tetrazole stationary phase achieved a remarkable 96.38 % orthogonality and was established and utilized in the preparative separation and purification of natural products. Finally, the constructed single stationary phase highly orthogonal RPLC × SFC system was successfully applied in the preparative separation and purification of natural diarylheptanoids from the Saxifraga tangutica target fraction and yielded four diarylheptanoids with purities exceeding 95 %.

Integration of Two-Dimensional Liquid Chromatography-Mass Spectrometry and Molecular Docking to Characterize and Predict Polar Active Compounds in Curcuma kwangsiensis.

Curcuma kwangsiensis, one species of Curcumae zedoaria Ros. c, is a commonly used traditional Chinese medicine (TCM) for treating cardiovascular disease, cancer, asthma and inflammation. Polar compounds are abundant in water decoction, which would be responsible for critical pharmacological effects. However, current research on polar compounds in Curcumae zedoaria Ros. c remains scarce. In this study, the polar fraction from Curcuma kwangsiensis was firstly profiled on G protein-coupled receptor 109A (GPR109A), β2-adrenergic receptor (β2-AR), neurotensin receptor (NTSR), muscarinic-3 acetylcholine receptor (M3) and G protein-coupled receptor 35 (GPR35), which were involved in its clinical indications and exhibited excellent β2-AR and GPR109A receptor activities. Then, an offline two-dimensional reversed-phase liquid chromatography (RPLC) coupled with the hydrophilic interaction chromatography (HILIC) method was developed to separate polar compounds. By the combination of a polar-copolymerized XAqua C18 column and an amide-bonded XAmide column, an orthogonality of 47.6% was achieved. As a result of coupling with the mass spectrometry (MS), a four-dimensional data plot was presented in which 373 mass peaks were detected and 22 polar compounds tentatively identified, including the GPR109A agonist niacin. Finally, molecular docking of these 22 identified compounds to β2-AR, M3, GPR35 and GPR109A receptors was performed to predict potential active ingredients, and compound 9 was predicted to have a similar interaction to the β2-AR partial agonist salmeterol. These results were supplementary to the material basis of Curcuma kwangsiensis and facilitated the bioactivity research of polar compounds. The integration of RPLC×HILIC-MS and molecular docking can be a powerful tool for characterizing and predicting polar active components in TCM.

Ion-pair Reversed-phase×Low-pH Reversed-phase Two-dimensional Liquid Chromatography for In-depth Proteomic Profiling

Ion-pair Reversed-phase×Low-pH Reversed-phase Two-dimensional Liquid Chromatography for In-depth Proteomic Profiling

On-line two-dimensional liquid chromatography hyphenated to mass spectrometry and ion mobility-mass spectrometry for the separation of carbohydrates from lignocellulosic biomass

Lignocellulosic biomass is a promising resource of renewable energy. Its transformation to ethanol requires efficient pretreatment leading to complex liquid mixtures made of hundreds of oxygenated analytes. A large part of the released compounds belong to the carbohydrates family. To overcome the complexity of such samples, a comprehensive on-line two-dimensional reversed-phase liquid chromatography hyphenated to high-resolution mass spectrometry (RPLC × RPLC-HRMS) was dedicated to the separation of carbohydrates and more specifically oligomers coming from pretreated lignocellulosic biomass. The first part of this study consisted in the optimization of such hyphenation (i.e. selection of stationary phases, mobile phases, sampling time, etc.). Then, the analytical method was applied to an industrial aqueous biomass product coming from the sulfuric acid-based pretreatment of a wheat straw. Around 70 well-resolved chromatographic peaks corresponding to oligomers were obtained. Occupation of the separation space between each chromatographic dimension was estimated to 75%. In the last part of this study, the interest of ion mobility-mass spectrometry in addition to RPLC × RPLC was discussed. Some examples highlighted the additional separation that can bring ion mobility to RPLC × RPLC-IMS-HRMS method. Using this four-dimensional hyphenation method, each analyte was described by two retention times, the collisional cross section and the molecular formula allowing to reach a level of detail never seen for biomass sample compositions.

Separation and identification of polyphenol compounds in propolis using offline 2D-RPLC/RPLC coupled with Q-TOF-mass spectrometry

Propolis is a resinous product collected by honey bees from plant-derived materials, with high content of polyphenols associated to various bioactivities. In this study, a powerful separation and identification method of polyphenol compounds from Chinese propolis samples were investigated using off-line two-dimensional reversed-phase liquid chromatography (2D-RPLC/RPLC) in combination with Q-TOF-MS. A Click OEG and an XTerra C18 column were employed for the first and second dimensional separation, respectively. The identification efficacy of 2D-RPLC/RPLC and unidimensional LC (1D-LC) were compared, and 81 components involving 60 polyphenol compounds were characterized by the former method. In contrast, only 36 peaks were detected by the 1D-LC method. The proposed method was demonstrated to be more efficient for the existence or absence of target compounds identification, and that would provide a promising means for accurate determination and quality evaluation of Chinese propolis.

Determination of Vitamins D2 and D3 in Edible Fungus by Reversed-Phase Two-Dimensional Liquid Chromatography

Vitamin D is the name given to a series of compounds with antirachitic activity. In this study, we developed a method for quantification of the common Vitamin D, ergocalciferol (vitamin D2), and cholecalciferol (vitamin D3), in edible fungus by reversed-phase two-dimensional liquid chromatography. The sample was saponified by KOH ethanol solution and extracted with ethyl acetate and n-hexane. After reconcentration, the sample was directly injected for instrumental analysis. The results showed that the spiking recoveries of vitamin D2 and vitamin D3 were 80.4–93.8% and 82.3–92.0%, respectively. The relative standard deviations (RSDs) were all less than 5%. Comparing to the results of isotope dilution liquid chromatography tandem mass spectrometry, there were no significant differences (P>0.05). The method was applied for testing vitamin D2 and D3 in 9 kinds of edible mushrooms. It showed that vitamin D3 was not detected. The content of vitamin D2 ranged from 0.11 μg/100 g to 123 μg/100 g. The content of vitamin D2 in dried mushroom was the highest, while that in fresh mushroom was the lowest. The limit of quantification was 0.025 μg/100 g.

High-throughput and Deep-proteome Profiling by 16-plex Tandem Mass Tag Labeling Coupled with Two-dimensional Chromatography and Mass Spectrometry.

Isobaric tandem mass tag (TMT) labeling is widely used in proteomics because of its high multiplexing capacity and deep proteome coverage. Recently, an expanded 16-plex TMT method has been introduced, which further increases the throughput of proteomic studies. In this manuscript, we present an optimized protocol for 16-plex TMT-based deep-proteome profiling, including protein sample preparation, enzymatic digestion, TMT labeling reaction, two-dimensional reverse-phase liquid chromatography (LC/LC) fractionation, tandem mass spectrometry (MS/MS), and computational data processing. The crucial quality control steps and improvements in the process specific for the 16-plex TMT analysis are highlighted. This multiplexed process offers a powerful tool for profiling a variety of complex samples such as cells, tissues, and clinical specimens. More than 10,000 proteins and posttranslational modifications such as phosphorylation, methylation, acetylation, and ubiquitination in highly complex biological samples from up to 16 different samples can be quantified in a single experiment, providing a potent tool for basic and clinical research.

Application of the new at-column dilution (ACD) modulator for the two-dimensional RP\xd7HILIC analysis of Buddleja davidii

The focus of this study was the analysis of the complex chemical composition from different parts of Buddleja davidii, whose species are commonly known as ornamental plants and herbal medicines in many countries. As an herbal medicine, it has been utilized for stroke treatments, headache, wound healing, neurological disorder, etc. However, the understanding of its chemical matrices is still insufficient. Therefore, an online two-dimensional reversed phase liquid chromatography x hydrophilic interaction liquid chromatography (RPLCxHILIC) system coupled with mass spectrometry was applied for further detailed investigation of the chemical constituents in Buddleja dividii. In this two-dimensional liquid chromatography (2D-LC) method, a new at-column dilution (ACD) modulator was introduced in the 2D-LC system to solve the incompatibility problem of the mobile phase between two dimensions, which resulted in a 2D-LC analysis with high orthogonality. For the root extract, as one of the analyzed samples, the optimization of the 1D and 2D gradients was carried out carefully. With this new modulator, much better peak separation and better peak shape were achieved compared to two-dimensional liquid chromatography system using a traditional standard (TS) modulator. With a similar approach, the other four parts of Buddleja davidii were well separated. Comparing the different analyzed parts, flowers and leaves showed the most complex profiles. MS and MS/MS data were obtained successfully, which demonstrated the potential of the proposed RPLCxHILIC-MS system in the constituents’ analysis of herbal medicine. However, due to the lack of reported reference information, 24 compounds could be tentatively identified.

Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples.

Two-dimensional reversed-phase capillary liquid chromatography (2D RPLC) separations have enabled comprehensive proteome profiling of biological systems. However, milligram sample quantities of proteins are typically required due to significant losses during offline fractionation. Such a large sample requirement generally precludes the application samples in the nanogram to low-microgram range. To achieve in-depth proteomic analysis of such small-sized samples, we have developed the nanoFAC (nanoflow Fractionation and Automated Concatenation) 2D RPLC platform, in which the first dimension high-pH fractionation was performed on a 75-μm i.d. capillary column at a 300 nL/min flow rate with automated fraction concatenation, instead of on a typically used 2.1 mm column at a 200 μL/min flow rate with manual concatenation. Each fraction was then fully transferred to the second-dimension low-pH nanoLC separation using an autosampler equipped with a custom-machined syringe. We have found that using a polypropylene 96-well plate as collection device as well as the addition of n-Dodecyl β-d-maltoside (0.01%) in the collection buffer can significantly improve sample recovery. We have demonstrated the nanoFAC 2D RPLC platform can achieve confident identifications of ∼49,000-94,000 unique peptides, corresponding to ∼6,700-8,300 protein groups using only 100-1000 ng of HeLa tryptic digest (equivalent to ∼500-5,000 cells). Furthermore, by integrating with phosphopeptide enrichment, the nanoFAC 2D RPLC platform can identify ∼20,000 phosphopeptides from 100 μg of MCF-7 cell lysate.

Off-line two-dimensional liquid chromatography coupled with diode array detection and quadrupole-time of flight mass spectrometry for the biotransformation kinetics of Ginkgo biloba leaves extract by diabetic rat liver microsomes

Ginkgo biloba leaves extract (GBE), one of the most widely used traditional Chinese medicines worldwide, can be used for the treatment of diabetes mellitus (DM). However, its biotransformation in liver is not fully known under the state of DM. In this study, an off-line hydrophilic interaction × reversed-phase two-dimensional liquid chromatography (HILIC × RP 2D-LC) system coupled with diode array detection (DAD) and quadrupole time-of-flight mass spectrometry (q/TOF-MS) was established for the qualification and quantification of the biotransformation of GBE in normal and diabetic rat liver microsomes (RLMs). 6 metabolites were tentatively identified according to the exact molecular weights and the characteristic fragment ions provided by q/TOF-MS data. The results of metabolic stability showed that the metabolic ratio of four target compounds including quercetin, genistein, kaempferol and isorhamnetin in diabetic RLMs were significantly enhanced when comparing with normal RLMs. The results of enzyme kinetics showed that compared with normal RLMs, the Michaelis-Menten constant (Km) value of genistein was obvious increased while its maximal velocity (Vmax) and intrinsic clearance (CLint) values were significantly decreased by diabetic RLMs, and the Vmax and CLint values of kaempferol and isorhamnetin were notably enhanced while their Km values were markedly reduced. For the half-time (t1/2) values of four target compounds and the Km, Vmax and CLint values of quercetin, there were not statistically significant changes between normal and diabetic RLMs. The results suggest that the developed off-line 2D LC-DAD-q/TOF-MS method is an easy and accurate approach for the study of GBE biotransformation in RLMs and may provide the essential data for further pharmacological and clinical studies of GBE.

Chemical Profiling and Comparison of Sangju Ganmao Tablet and Its Component Herbs Using Two-Dimensional Liquid Chromatography to Explore Compatibility Mechanism of Herbs.

Sangju Ganmao tablet (SGT), a well-known Chinese patent medicine used to treat cold symptoms, is made from eight herbal medicines. In this study, an off-line hydrophilic interaction × reversed-phase two-dimensional liquid chromatography (HILIC × RP 2D-LC) method was developed to comprehensively separate the chemical constituents of SGT. Through optimization of the experimental conditions, a total of 465 peaks were finally detected in SGT, and the structures of 54 selected compounds were fully identified or tentatively characterized by quadrupole time-of-flight mass spectrometry (qTOF-MS) analysis. The established 2D-LC analysis showed high orthogonality (63.62%) and approximate 11-fold improvement in peak capacity (2399 and 1099, obtained by two calculation methods), in contrast to conventional one-dimensional RPLC separation. The eight component herbs of SGT were also respectively separated by using the 2D-LC system, and we found that a total of 12 peaks detected in SGT were not discovered in any component herbs. These newly generated chemical constituents would benefit better understanding of the compatibility mechanism of the component herbs. The strategy established in this study could be used for systematic chemical comparison of SGT and its component herbs, which contributes to exploration of herbal compatibility mechanism.

Separation of lignans from Schisandra chinensis by two-dimensional reversed-phase liquid chromatography

A two-dimensional reversed-phase liquid chromatography (2D-RPLC) method was established to separate lignan components and pure compounds from Schisandra chinensis. This method was based on the modules of separation-enrichment and self-developed with independent intellectual property rights. First, a C18 column (250 mm×4.6 mm, 5 μm) was used as the analytical column. A water-methanol mixture was selected as the mobile phase. Separation resolution and retention time were selected as indexes. Gradient chromatography of the lignan extracts was repeated four times and the information was input into XTool, a chromatographic separation software. The conditions for the first-and second-dimensional chromatographic separation were optimized by XTool. Then, linear amplification was used for preparative chromatography. C18 column (250 mm×30 mm, 10 μm) was selected as the first-and second-dimensional separation column. The C18 columns (80 mm×30 mm, 10 μm) were selected as enriching columns, and water was chosen as the diluent solution. Lignans from Schisandra chinensis were separated and purified by 2D-RPLC. Finally, nine lignan components were obtained by the first-dimensional separation. Totally, 20 high-purity compounds, containing six monomers, were obtained by the second-dimensional separation. Experimental results showed that this method has good reproducibility. This method thus allows for the systematic separation of lignans from Schisandra chinensis.

Comprehensive on-line two-dimensional liquid chromatography × supercritical fluid chromatography with trapping column-assisted modulation for depolymerised lignin analysis

Lignin depolymerisation produces a large variety of low molecular weight phenolic compounds that can be upgraded to value-added chemicals. Detailed analysis of these complex depolymerisation mixtures is, however, hampered by the lack of resolving power of traditional analysis techniques. In this study, a novel online comprehensive two-dimensional reversed-phase liquid chromatography (RPLC) × supercritical fluid chromatography (SFC) method with trapping column interface was developed for the separation of phenolic compounds in depolymerised lignin samples. The trapping capacities of different trapping columns were evaluated. The influence of large volume water-containing injection on SFC performance was studied. The relation between peak capacity and first dimension flow rate and gradient was investigated. The optimized method was applied for the analysis of a depolymerised lignin sample. The RPLC × SFC system exhibited high degree of orthogonality. Compared with traditional loop based interface, trapping column interface can significantly shorten the analysis time and offer higher detectability, with the disadvantage of more severe undersampling in the first dimension.

Optimizing gradient conditions in online comprehensive two-dimensional reversed-phase liquid chromatography by use of the linear solvent strength model.

The linear solvent strength model was used to predict coverage in online comprehensive two-dimensional reversed-phase liquid chromatography. The prediction model uses a parallelogram to describe the separation space covered with peaks in a system with limited orthogonality. The corners of the parallelogram are assumed to behave like chromatographic peaks and the position of these pseudo-compounds was predicted. A mix of 25 polycyclic aromatic compounds were used as a test. The precision of the prediction, span 0-25, was tested by varying input parameters, and was found to be acceptable with root mean square errors of 3. The accuracy of the prediction was assessed by comparing with the experimental coverages. Less than half of experimental coverages were outside prediction ± 1 × root mean square error and none outside prediction ± 2 × root mean square error. Accuracy was lower when retention factors were low, or when gradient conditions affected parameters not included in the model, e.g. second dimension gradient time affects the second dimension equilibration time. The concept shows promise as a tool for gradient optimization in online comprehensive two-dimensional liquid chromatography, as it mitigates the tedious registration and modeling of all sample constituents, a circumstance that is particularly appealing when dealing with complex samples.

Separation and characterization of chemical constituents in Ginkgo biloba extract by off-line hydrophilic interaction × reversed-phase two-dimensional liquid chromatography coupled with quadrupole-time of flight mass spectrometry

Ginkgo biloba extract (GBE), derived from the leaves of Ginkgo biloba L., is one of the most widely used traditional Chinese medicines worldwide. Due to high structural diversity and low abundance of chemical constituents in GBE, conventional reversed-phase liquid chromatography has limited power to meet the needs of its quality control. In this study, an off-line hydrophilic interaction×reversed-phase two-dimensional liquid chromatography (HILIC×RP 2D-LC) system coupled with diode array detection (DAD) and quadrupole time-of-flight mass spectrometry (qTOF-MS) was established to comprehensively analyze the chemical constituents of GBE. After optimizing the chromatographic columns and mobile phase of 2D-LC, a Waters XBridge Amide column using acetonitrile/water/formic acid as the mobile phase was selected as the first dimension to fractionate GBE, and the obtained fractions were further separated on an Agilent Zorbax XDB-C18 column with methanol/water/formic acid as the mobile phase. As a result, a total of 125 compounds were detected in GBE. The orthogonality of the 2D-LC system was 69.5%, and the practical peak capacity was 3864 and 2994, respectively, calculated by two different methods. The structures of 104 compounds were tentatively characterized by qTOF-MS analysis, and 21 of them were further confirmed by comparing with reference standards. This established HILIC×RP 2D-LC-qTOF/MS system can greatly improve the separation and characterization of natural products in GBE or other complicated herbal extracts.

Optimization of conditions in on-line comprehensive two-dimensional reversed phase liquid chromatography. Experimental comparison with one-dimensional reversed phase liquid chromatography for the separation of peptides

Comprehensive on-line two-dimensional liquid chromatography is an attractive technique to enhance peak capacity and deal with complex samples. Yet, its optimization is not straightforward and requires to take into account a huge number of parameters to finally obtain a good compromise between different criteria which are often conflicting. In this study, we propose a procedure for RPLC×RPLC separations able to define, for a given analysis time, the optimized LC×LC parameters for achieving the best compromise between high peak capacity and low dilution. This procedure makes use of both a prediction tool based on theoretical relationships and a Pareto-optimality approach to optimize these two criteria. The possibility to split the flow-rate of the first dimension before the interface is taken into account as well as the focusing effect in the second dimension. This optimization procedure is applied to the prediction of optimized conditions for the separation of peptides. The need for very short and efficient columns (typically 30mm as column length and 1.3μm as particle diameter) in the second dimension is clearly established whatever the geometry of the first dimension column. Furthermore it is shown that several sets of quite different conditions in the first dimension can lead to similar results and hence that additional quality descriptors are required to make a decision. RPLC×RPLC separations of a protein digest were carried out and the obtained results were found in very good accordance with the predicted ones. Our results were compared to the top results reported in the literature for 1D-RPLC separations of peptides. More than 4-fold increase in peak capacity (5100 vs 1150) at 200min has been obtained. Furthermore a 40-fold gain in analysis time (1h vs 40h) was obtained for achieving 1800 as effective peak capacity which is close to the highest peak capacity reported in 1D-RPLC for the separation of peptides.

Quantitative proteomics of bronchoalveolar lavage fluid in idiopathic pulmonary fibrosis.

The proteomic analysis of bronchoalveolar lavage fluid (BALF) can give insight into pulmonary disease pathology and response to therapy. Here, we describe the first gel-free quantitative analysis of BALF in idiopathic pulmonary fibrosis (IPF), a chronic and fatal scarring lung disease. We utilized two-dimensional reversed-phase liquid chromatography and ion-mobility-assisted data-independent acquisition (HDMSE) for quantitation of >1000 proteins in immunodepleted BALF from the right middle and lower lobes of normal controls and patients with IPF. Among the analytes that were increased in IPF were well-described mediators of pulmonary fibrosis (osteopontin, MMP7, CXCL7, CCL18), eosinophil- and neutrophil-derived proteins, and proteins associated with fibroblast foci. For additional discovery and targeted validation, BALF was also screened by multiple reaction monitoring (MRM), using the JPT Cytokine SpikeMix library of >400 stable isotope-labeled peptides. A refined MRM assay confirmed the robust expression of osteopontin, and demonstrated, for the first time, upregulation of the pro-fibrotic cytokine, CCL24, in BALF in IPF. These results show the utility of BALF proteomics for the molecular profiling of fibrotic lung diseases and the targeted quantitation of soluble markers of IPF. More generally, this study addresses critical quality control measures that should be widely applicable to BALF profiling in pulmonary disease.

Off-line two-dimensional liquid chromatography for metabolomics: an example using Agaricus bisporus mushrooms exposed to UV irradiation

It has previously been shown that irradiation with UV light increases the vitamin D content of certain mushroom species, but the effect on other nutrients is unknown, and is difficult to assess due to the complexity of the sample matrix. Here, an offline reversed phase × reversed phase two-dimensional liquid chromatography methodology was developed and applied to Agaricus bisporus mushrooms in order to demonstrate the potential of the technique and assess the effect of UV irradiation on the mushroom’s metabolic profile. The method allowed the detection of 158 peaks in a single analytical run. A total of 51 compounds including sugars, amino acids, organic and fatty acids and phenolic compounds were identified using certified reference standards. After irradiation of the mushrooms with UV for 30 s the number of peaks detected decreased from 158 to 150; 47 compounds increased in concentration while 72 substances decreased. This is the first time that two-dimensional liquid chromatography has been carried out for the metabolomic analysis of mushrooms. The data provide an overview of the gain/loss of nutritional value of the mushrooms following UV irradiation and demonstrate that the increased peak capacity and separation space of two-dimensional liquid chromatography has great potential in metabolomics.

A not-stop-flow online normal-/reversed-phase two-dimensional liquid chromatography–quadrupole time-of-flight mass spectrometry method for comprehensive lipid profiling of human plasma from atherosclerosis patients

A not-stop-flow online two-dimensional (2D) liquid chromatography (LC) method was developed for comprehensive lipid profiling by coupling normal- and reversed-phase LC with quadrupole time-of-flight mass spectrometry (QToF-MS), which was then applied to separate and identify the lipid species in plasma, making its merits in quality and quantity of the detection of lipids. Total 540 endogenous lipid species from 17 classes were determined in human plasma, and the differences in lipid metabolism products in human plasma between atherosclerosis patients and control subjects were explored in detail. The limit of detections (LODs) of 19 validation standards could all reach ng/mL magnitude, and the RSDs of peak area and retention time ranged 0.4–8.0% and 0.010–0.47%, respectively. In addition, a pair of isomers, galactosylceramides (GalC) and glucosylceramides (GluC), was successfully separated, showing that only the levels of GalC in atherosclerosis patients were significantly increasing, rather than GluC, compared with the controls (controls vs. patients: the ratio was 1.5–2.8-fold increasing). It would be helpful to the further research of the atherosclerosis.

Effective 2D-RPLC/RPLC enrichment and separation of micro-components from Hedyotis diffusa Willd. and characterization by using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry

An effective method aiming at enrichment and analysis of micro-components in traditional Chinese medicine (TCM) was developed. One fraction (fraction E) from the extract of Hedyotis diffusa Willd. was selected as test sample, which was isolated by using the XAD-4 macroporous resin. To study the micro-components, a two-dimensional reverse-phase liquid chromatography (2D-RPLC/RPLC) method was developed, comprising Click OEG and C18 stationary phases as the first and second dimensions, respectively. Of the eight sub-fractions isolated from the first dimension, three sub-fractions (fractions II–IV) containing micro-components were further separated with the second dimension. The 2D-RPLC/RPLC system was proved to possess high orthogonality. Furthermore, the micro-components were characterized by using ultra-performance liquid chromatography–diode array detector/quadrupole time-of-flight mass spectrometry (UPLC–DAD/Q-TOF MS) with electrospray ionization (ESI) source. With the optimized separation and characterization method, a large number (>400) of micro-components were enriched and detected from the extracts of H. diffusa Willd., the majority of which has not been isolated from the herb before. Among these isolated micro-components, 38 compounds involving 24 phenylpropanoids, 7 flavonoids and 7 iridoid glucosides (IGs), were identified or tentatively identified from the H. diffusa extracts on the basis of spectral data of the authentic standards and the fragmentation characteristics information available in literatures. The proposed method made it possible to effectively screen and analyze the micro-components in TCMs or other complex natural medicines.