Recent advances in capillary separations for proteomics

The sequencing of several organisms' genomes, including the human's one, has opened the way for the so-called postgenomic era, which is now routinely coined as "proteomics". The most basic task in proteomics remains the detection and identification of proteins from a biological sample, and the most traditional way to achieve this goal consists of protein separations performed by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Still, the 2-D PAGE-mass spectrometry (MS) approach remains lacking in proteome coverage (for proteins having extreme isoelectric points or molecular masses as well as for membrane proteins), dynamic range, sensitivity, and throughput. Consequently, considerable efforts have been devoted to the development of non-gel-based proteome separation technologies in an effort to alleviate the shortcomings in 2-D PAGE while reserving the ability to resolve complex protein and peptide mixtures prior to MS analysis. This review focuses on the most recent advances in capillary-based separation techniques, including capillary liquid chromatography, capillary electrophoresis, and capillary electrokinetic chromatography, and combinations of multiples of these mechanisms, along with the coupling of these techniques to MS. Developments in capillary separations capable of providing extremely high resolving power and selective analyte enrichment are particularly highlighted for their roles within the broader context of a state-of-the-art integrated proteome effort. Miniaturized and integrated multidimensional peptide/protein separations using microfluidics are further summarized for their potential applications in high-throughput protein profiling toward biomarker discovery and clinical diagnosis.     

An immobiline DryStrip application method enabling high-capacity two-dimensional gel electrophoresis

In the field of proteomics the need to detect low-abundance cellular components, such as regulatory proteins, is of critical importance. Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) is one of the most commonly used separation tools for these biological investigations. In this paper we report an alternative micropreparative 2-D PAGE sample application method, called the "paper bridge loading" method. This method makes it possible to apply a larger sample volume to commercially available immobilized pH gradient (IPG) strips. The Vh products required for focusing are only marginally longer than those used in analytical experiments. The method was compared to traditional cup loading and in-gel rehydration. With 18 cm long narrow-range Immobiline DryStrip pH 4.5-5.5, the "paper bridge" method allowed the application of 10 mg human plasma proteins compared to 3 mg with traditional loading methods. The corresponding figures using Escherichia coli sample was found to be 6 mg and less than 2 mg, respectively. The paper bridge method also showed the best results in terms of spot resolution and separation of high molecular weight proteins.     

Qualitative and quantitative analysis in quality control of traditional Chinese medicines

Separation techniques with high efficiency and sensitive detection have been widely used for quality control of traditional Chinese medicines (TCMs). High-performance liquid chromatography, gas chromatography, and capillary electrophoresis are commonly used to separate various components in TCMs. Ultraviolet detection, fluorescence detection, evaporative light-scattering detection, mass spectrometry and nuclear magnetic resonance can be applied to separation techniques for qualitative and quantitative analysis of TCMs. The development of quality control for TCMs based on quantitative and qualitative analysis from 2000 to 2007 are reviewed; the fingerprint technique is also discussed due to its broad application in the quality control of TCMs. Prospects for further research based on our primary results are also discussed.     

Comprehensive two-dimensional HPLC to study the interaction of multiple components in Rheum palmatum L. with HSA by coupling a silica-bonded HSA column to a silica monolithic ODS column

A mode of comprehensive 2-D LC was developed by coupling a silica-bonded HSA column to a silica monolithic ODS column. This system combined the affinity property of the HSA column and the high-speed separation ability of the monolithic ODS column. The affinity chromatography with HSA-immobilized stationary phase was applied to study the interaction of multiple components in traditional Chinese medicines (TCMs) with HSA according to their affinity to protein in the first dimension. Then the unresolved components retained on the HSA column were further separated on the silica monolithic ODS column in the second dimension. By hyphenating the 2-D separation system to diode array detector and MS detectors, the UV and molecular weight information of the separated compounds can also be obtained. The developed separation system was applied to analysis of the extract of Rheum palmatum L., a number of low-abundant components can be separated on a single peak from the HSA column after normalization of peak heights. Six compounds were preliminarily identified according to their UV and MS spectra. It showed that this system was very useful for biological fingerprinting analysis of the components in TCMs and natural products.     

Ongoing development of two-dimensional polyacrylamide gel electrophoresis data standards

We present an approach toward standardizing two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) data in support of developing a globally relevant proteomics consensus in order to provide more efficient database querying and data comparisons through the establishment of the necessary definitions and interdisciplinary reference fields for both the 2-D PAGE community, particularly in the proteomics area, and the clinical and experimental biological research communities, in general. This article covers the need for unifying the 2-D PAGE data through a common data repository, and its usefulness in data standards and data interoperability.     

Affinity chromatography with immobilized DNA stationary phase for biological fingerprinting analysis of traditional Chinese medicines

A stationary phase for high performance affinity chromatography with immobilization of DNA onto silica gel was prepared and characterized. The effect of the ionic strength, concentration of Mg2+, EDTA and CH3CN in the mobile phase on the retention of alkaloids were investigated. With this stationary phase, biological fingerprinting analysis of traditional Chinese medicines (TCMs) Coptis chinensis Franch and Rheum palmatum L. was performed with both one-dimensional (1-D) and two-dimensional (2-D) chromatography. The 1-D chromatography was performed with isocratic and gradient elution and 2-D chromatography was developed with immobilized DNA column combined with silica monolithic ODS column. It was found that 7 compounds in Coptis chinensis Franch including berberine, palmatine and jatrorrhizine, 14 compounds in Rheum palmatum L. including aloe-emodin, rhein, emodin, chrysophannol-8-O-glucophranoside and physionl-8-O-glucophranoside were active in binding to the immobilized DNA.     

中药物质基础的高效液相色谱分离分析方法研究

高效液相色谱方法已成为中药物质基础研究的重要手段．在中药质量控制、中药标准品制备、活性化合物发现等方面发挥着不可替代的作用．然而我们的实验数据表明,一个中药材可能包含上万个化合物．中药物质基础的复杂性对高效液相色谱方法提出了巨大挑战．本文针对液相色谱方法在中药物质基础分离分析中存在的问题与难点,结合红花、黄连、姜黄三味药材样品,从亲水色谱分离模式、新型色谱固定相、二维液相色谱分离系统和液相色谱质谱联用技术等方面讨论了液相色谱的分离分析方法和发展方向．结果表明,高效液相色谱新技术新方法在中药复杂体系的分离分析中具有很大的发展潜力和应用前景．     

Hydrophilic interaction liquid chromatography (HILIC) in proteomics

In proteomics, nanoflow multidimensional chromatography is now the gold standard for the separation of complex mixtures of peptides as generated by in-solution digestion of whole-cell lysates. Ideally, the different stationary phases used in multidimensional chromatography should provide orthogonal separation characteristics. For this reason, the combination of strong cation exchange chromatography (SCX) and reversed-phase (RP) chromatography is the most widely used combination for the separation of peptides. Here, we review the potential of hydrophilic interaction liquid chromatography (HILIC) as a separation tool in the multidimensional separation of peptides in proteomics applications. Recent work has revealed that HILIC may provide an excellent alternative to SCX, possessing several advantages in the area of separation power and targeted analysis of protein post-translational modifications. Figure Artistic impression of the HILIC separation mechanism     

Comprehensive two-dimensional high performance liquid chromatography system with immobilized liposome chromatography column and monolithic column for separation of the traditional Chinese medicine Schisandra chinensis

A comprehensive two-dimensional (2D) separation is one that employs two separation dimensions (columns) and draws on all of the available resolving power from each of the dimensions of separate the components in a sample. In this study, a comprehensive 2D chromatography approach was developed for the separation and identification of membrane permeable compounds in a famous traditional Chinese medicine of Schisandra chinensis. The first dimensional column was the immobilized liposome chromatography (ILC) column, which mimics the biological membranes and can be used to study drug-membrane interactions in liquid chromatography. Using an automatic ten-port switching valve equipped with two sample loops, the section of the first-dimension was introduced in the second-dimension consist of a silica monolithic column. More than 40 components in Schisandra chinensis were resolved by using the developed separation system and among them 14 compounds were identified interacting with the ILC column based on their retention action, UV and mass data. With this comprehensive 2D-HPLC system, the three-dimensional chromatographic fingerprints of Schisandra chinensis were preliminarily established and processed by using principal component analysis and hierarchical clustering analysis. The obtained information can distinguish the unacceptable samples of the quality control. The result demonstrated that the 2D biochromatography system has been demonstrated to have more advantages of finding strong binding bioactive components, providing an enhanced peak capacity, good sensitivity and powerful resolution biological fingerprinting analysis of complex TCMs, which was a useful means to control the quality of and to clarify the membrane permeability of the compounds in Schisandra chinensis.     

中药质量控制技术发展展望

本文从中药产业需求、现代化需求、技术需求、机遇与挑战等方面概括了中药质量控制技术发展的背景;讨论了中药质量控制技术对于提高中药药效和安全性、推动产业发展和推进中药国际化的意义;综述了中药质量控制技术的现状,分析了在过程控制、安全性控制、标准品和对照品制备、指纹图谱技术等方面的不足;提出了中药质量控制技术应重点发展以分离和表征技术为主的中药质量控制关键技术、中药安全性控制技术、中药质量控制标准体系、中药质量控制原创性技术和中药标准品、对照品生产技术,制定技术标准,建立具有中药特色的过程控制和产品质量控制标准。     

复杂生物体系中蛋白质高效分离分析技术的新进展

继人类基因组计划完成之后,作为一种新的研究策略,蛋白质组学在生命科学研究中发挥着愈来愈重要的作用。由于生物体系的复杂性和多样性,使得分离效率高、灵敏度高、通量高和动态范围宽的分离分析技术平台的研究和应用已成为蛋白质组学研究的重点和热点之一。着重介绍了近年来应用日益广泛的多维色谱预分离、毛细管液相色谱-质谱联用、毛细管电泳及其与质谱联用等高效分离分析技术在复杂生物体系的蛋白质分析中的最新进展。引用相关文献40篇。     

Two-dimensional difference gel electrophoresis applied for analytical proteomics: fundamentals and applications to the study of plant proteomics

The present review reports the principles, fundamentals and some applications of two-dimensional difference gel electrophoresis for analytical proteomics based on plant proteome analysis, also emphasizing some advantages of 2-D DIGE over 2-D PAGE techniques. Some fluorescent protein labeling reagents, methods of protein labeling, models of 2-D DIGE experiments, and some limitations of this technique are presented and discussed in terms of 2-D DIGE plant proteomes. Finally, some practical applications of this technique are pointed out, emphasizing its potentialities in plant proteomics.     

Novel liquid-chromatography columns for proteomics research

The enormous interest in proteomics research in recent years has inspired many developments in peptide chromatography. Different strategies have been developed to cope with the vast complexity of proteomics samples, trying to provide sufficient degree of separation to be able to exploit fully the potential of protein identification by mass spectrometry (MS). As reversed-phase liquid chromatography (RPLC) coupled to MS is still the method of choice for the analysis of protein digests, many efforts focus on the development of high-efficiency RP methods (e.g., monolithic columns and ultra-high-performance LC). This can also increase the speed and the sensitivity of the analysis of protein digests.As RPLC-MS alone is unlikely to provide sufficient resolution to unravel the composition of highly complex samples comprehensively, multidimensional methods will remain essential in proteome research. In this area, hydrophilic interaction chromatography (HILIC) seems to be a promising alternative to the traditional strong cation-exchange-based methods. Also, HILIC has found application in the analysis of post-translational modifications (e.g., phosphorylation and glycosylation).This review describes recent developments in LC methods for proteomics research, focusing on advances in column technology and the application of novel column materials. Illustrative examples show the possibilities of the new columns in proteomics research.     

Screening and analysis of bioactive compounds with biofingerprinting chromatogram analysis of traditional Chinese medicines targeting DNA by microdialysis/HPLC

Biofingerprinting chromatogram analysis, which is defined as the comparison of fingerprinting chromatograms of the extract of traditional Chinese medicines (TCMs) before and after the interaction with biological systems (DNA, protein, cell, etc.), was proposed for screening and analysis of the multiple bioactive compounds in TCMs. A method of microdialysis sampling combined with high performance liquid chromatography (HPLC) was applied to the study of DNA-binding property for the extracts of TCMs. Seven compounds were found to bind to calf thymus DNA (ct-DNA) from the TCMs of Coptis chinensis Franch (Coptis), but only three ones from Phellodendron amurense Rupr. (Phellodendron) and none from Sophoraflavescens Ait. (Sophora) to bind to ct-DNA, respectively. Three of them were identified as berberine, palmatine and jatrorrhizine and their association constants (K) to ct-DNA were determined by microdialysis/HPLC. Competitive binding behaviors of them to ct-DNA were also investigated.     

Fingerprint analysis of Ligusticum chuanxiong using hydrophilic interaction chromatography and reversed-phase liquid chromatography

Fingerprint analysis is considered one of the most powerful approaches to quality control in traditional Chinese medicines (TCMs). In this study, a binary chromatographic fingerprint analysis was developed using hydrophilic interaction chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) to gain more chemical information about polar compounds and weakly polar compounds. This method was used to construct a chromatographic fingerprint of Ligusticum chuanxiong. The two chromatographic methods demonstrated good precision, reproducibility, and stability, with relative standard deviations of <2% for retention time and 7% for peak area for both HILIC and RPLC separations. Data from the analysis of 14 samples by HILIC and RPLC were processed with similarity analysis, with correlation coefficients and congruence coefficients. This binary fingerprint analysis, using two chromatographic modes, is a powerful tool for characterizing the quality of samples, and can be used for the comprehensive quality control of TCMs.     

Two-dimensional strong cation-exchange liquid chromatography/reversed-phase pressurized capillary electrochromatography for separation of complex samples

A 2-D separation platform was constructed using micro strong cation-exchange liquid chromatography (μ-SCXLC) and reversed-phase pressurized capillary electrochromatography (RP-pCEC) for the analysis of complex samples. Samples were fractionated by the first-dimension μ-SCXLC with a linear solvent gradient and then injected into the second-dimension RP-pCEC for further separation. The μ-SCXLC/RP-pCEC 2-D system with three separation mechanisms, namely strong cation-exchange, reversed-phase chromatography and electrophoresis, provided high selectivity, high resolution and high peak capacity compared to one-dimensional chromatographic approaches. Separation effectiveness of this 2-D system was demonstrated by the analysis of different kinds of complex samples, such as traditional Chinese medicine Cortex Phellodendri, bovine serum albumin (BSA) tryptic digest and real serum tryptic digest. A theoretical peak capacity of approximately 1200 was achieved, which proves its promising potential for the separation and analysis of complex samples.     

Purification of polar compounds from Radix isatidis using conventional C18 column coupled with polar-copolymerized C18 column

Regarding hydrophilic interaction chromatography and normal phase liquid chromatography, RPLC is another choice used to separate polar compounds with the improvement of polar-modified C18 stationary phase. In this study, a method using conventional C18 column coupled with polar-copolymerized C18 column was successfully developed for the separation and purification of polar compounds from Radix isatidis, which is one of the most commonly used traditional Chinese medicines (TCMs). An XTerra MS C18 column was used to fractionate the extract of R. isatidis and a homemade polar-copolymerized C18 column was utilized for the final purification due to its good separation selectivity and high resolution for polar compounds. The established purification system demonstrated good orthogonality for the polar compounds. As a result, ten compounds were purified and three of them were identified as 3-methyl-5-vinyloxazolidin-2-one (compound A), 5-hydroxymethyl-2-furaldehyde (compound B) and 3-methylfuran-2-carboxylic acid (compound G) based on the MS, IR and extensive NMR data, respectively. It was demonstrated to be a feasible and powerful technique for the purification of polar compounds under RPLC mode and more chemical information of TCMs will be obtained to interpret the efficiency of TCMs.     

Application of two‐dimensional liquid chromatography in the separation of traditional Chinese medicine

Traditional Chinese medicines have been widely used to prevent and cure diseases for thousands of years. For the purpose of better understanding the extremely complicated traditional Chinese medicines, powerful separation techniques are essential. Two‐dimensional liquid chromatography has been proven to be more powerful for the separation of complex traditional Chinese medicines due to its enhanced peak capacity and resolution compared with one‐dimensional liquid chromatography. Enormous efforts have been made on the coupling of independent separation mechanisms to improve the resolving power for complex traditional Chinese medicine samples, including the development and introduction of novel stationary phases. This review aims to give an overview on the applications of two‐dimensional liquid chromatography in traditional Chinese medicine research since 2008, including comprehensive two‐dimensional liquid chromatography, heart‐cutting two‐dimensional liquid chromatography both in on‐line, and off‐line mode. Different couplings of separation modes were respectively discussed based on specific studies, with emphasis on the applications of novel stationary phases in the two‐dimensional liquid chromatography.     

中药分析新思路及其质量控制

随着国家对中药现代化的重视,为了更好地诠释中药药性的本质,研究者从不同角度对中药进行研究。分析化学、药学、生物学等多学科的多种不同的技术在这里融合,一些新的思路和方法正在不断涌现,中药的分析与质量控制正沿着综合且全面的方向在不断地发展和前进。该文对当前中药分析新思路及其质量控制进行了简要评述,在此基础上,对中药质量控制的色谱指纹图谱进行了分类说明与研究,表明采用现代分析手段,可以实现对中药质量的有效控制。     

Feasibility of sterilizing traditional Chinese medicines by gamma-irradiation

The feasibility of sterilizing traditional Chinese medicine (TCMs) by γ-irradiation has been systematically evaluated by the biological, toxicological and physicochemical tests on irradiated hundreds of TCMs. Those TCMs investigated in general show no significant biological or toxicological changes after irradiation, yet physicochemical changes are detectable in some irradiated TCMs, and water in TCMs enhances the effects. Those results obtained from radiolysis of some major effective components of TCMs in aqueous or ethanolic solutions reveal that the site selection of radiolytically generated radicals follows the example of simple compounds with same function groups. Wholesomeness and chemical clearance present a bright future to sterilizing TCMs by γ irradiation, however, some important measures and steps should be adopted: (1) The producers must strictly execute manufacturing procedure to reduce microbiological contamination thus lower the applied dose for sterilization which is recommended to be controlled under 5, 7 or 10 kGy, 10 kGy for dry herb, 7 kGy for herbal medicine and 5 kGy for some special herbal medicine; (2) Herb to be sterilized by γ-irradiation should exist in possible dry state; (3) Powder TCMs is recommended to mix with honey forming bolus, which can minimize the decomposition of herb.