基于强阳离子交换色谱与等电聚焦的磷酸化蛋白质组学分离策略比较

比较分析了强阳离子交换(SCX)与等电聚焦(IPG-IEF)技术在磷酸化蛋白质组学中的应用。采用3种标准磷酸化蛋白对SCX与IPG-IEF两种技术对磷酸化肽段富集的有效性进行考察。以HepG2细胞为复杂样本,考察SCX与IPG-IEF在实际样本中的应用情况。对SCX与IPG-IEF技术在18O标记的磷酸化蛋白质组定量研究中的应用情况进行考察。蛋白鉴定采用高准确度、高灵敏度、高分辨率的LTQ-FTICR-MS/MS质谱仪。实验表明:SCX和IPG-IEF在大规模磷酸化肽段分离过程中均有效;在复杂样本中,SCX技术的分离效果优于IPG-IEF;IPG-IEF的重复性好于SCX;在磷酸化蛋白质组定量分析结果表明,IPG-IEF技术的稳定性优于SCX。本研究为根据不同实验目的而选择适当的磷酸化蛋白质组预分离技术提供了有用信息。     

18O稳定同位素标记定量蛋白质组研究技术的建立与优化

建立了18O稳定同位素标记方法,用于复杂体系蛋白质相对定量分析。对影响蛋白质标记稳定性的实验条件进行了比较和优化。结果表明,采用酶切后标记的方法,酶切肽段在胰酶催化下,在pH 5.0的K2HPO4/KH2PO4缓冲体系中,37℃18O标记反应16 h,绝大部分肽段即可达到100%的标记效率。对多个16O/18O成对肽段峰强度的动态范围及定量准确度进行了考察。结果表明,18O标记方法是一种简便、稳定、可靠的相对定量方法,10倍动态范围内,标记率相对标准偏差在18.4%以内,16O/18O峰强度呈很好的线性关系。本实验考察了标记后的肽段在不同溶液体系中的稳定性,为复杂样品的预处理和预分离的溶液条件提供了依据。     

基于稳定同位素标记与质谱分析的蛋白质定量算法研究进展

蛋白质定量研究已成为蛋白质组学的热点,它是疾病相关生物标志物发现的重要途径.基于稳定同位素标记的质谱分析技术是蛋白质定量最常用的方法之一.随着实验方法的发展和改进,定量数据处理方法也在不断更新与完善.一般来说,定量数据处理包括四步:搜库鉴定、图谱定量信息提取与计算、肽段丰度比计算和蛋白质丰度比计算及差异显著性分析,其中后三步是数据处理的核心.目前,后三步中每步都有多种可选算法,这些算法一般都是针对特定实验技术而提出的,缺乏深入的工作对它们进行系统比较和优化.为此,在总结目前主要实验技术方法的基础上,论述了定量算法的现状和存在问题,并针对一些问题提出了可行的解决办法.     

等电聚焦预分离用于肝癌细胞分泌蛋白质组的分级与鉴定

分泌蛋白质组(secretome)是指在特定的时空条件下,细胞、组织等分泌的全部蛋白质。分泌蛋白质组可能包含了大量的疾病诊断生物标志物,因此其相关研究越来越受到重视。分泌蛋白质组的组成高度复杂且浓度范围宽,这对分析方法提出了挑战。建立有效的蛋白质或肽段预分离策略,将有利于分泌蛋白质的高覆盖率鉴定。本研究以肝癌细胞系MHCC97L的无血清培养分泌蛋白质为研究对象,采用一种新型等电聚焦预分离(OFFGEL)系统,考察了肽段水平的分级对蛋白质鉴定结果的影响。结果表明,分离后各馏分中肽段的等电点分布与理论预测基本一致,每个馏分中单独鉴定的肽段比例接近80%,显示了该系统对肽段的高分辨分离能力。结合生物质谱技术,在肝癌细胞分泌系统中鉴定了2995个蛋白质,显示了该系统在复杂体系蛋白质组研究中的应用潜力。     

基于生物质谱的乙酸酐稳定同位素标记定量蛋白质组学方法的建立与优化

建立了一种基于生物质谱的乙酸酐稳定同位素标记,定量蛋白质组学研究方法,优化了影响标记效率的各种条件。在pH8.0的Na2B4O7/H3BO3缓冲体系中,当乙酸酐摩尔浓度25倍过量于肽段摩尔量,22℃反应30 min时,标记即可完全。对多对H6/D6-乙酸酐标记肽段在基质辅助激光解吸电离质谱中的动态范围及定量准确度进行了考察,并通过串联质谱分析确定了乙酰化位点。结果表明:在10倍和30倍动态范围内,线性关系良好(r=0.99,r=0.98),理论值和观测值的偏差分别为0.5%和20%。     

18O同位素标记定量肽段串联体蛋白质结合同位素稀释-多反应监测质谱的蛋白质绝对定量新方法

建立了定量肽段串联体蛋白质(concatamers of Q peptides, QconCATs)结合¹⁸O同位素标记-多反应监测质谱的蛋白质绝对定量新方法。首先对QconCAT重组蛋白质进行了纯度表征,十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE)表征结果表明重组蛋白质的纯度在99%以上,相对分子质量约为63.4 kDa。对QconCAT重组蛋白质酶切后的肽段混合物进行质谱分析,并经pFind和pLabel软件处理,验证了目标肽段。还考察了QconCAT重组蛋白质的酶切效率和¹⁸O标记效率,并对QconCAT蛋白质结合¹⁸O标记-同位素稀释-多反应监测质谱方法进行了评价。实验结果表明,采用该方法对腾冲嗜热厌氧菌(Thermoanaerobacter tengcongensis, TTE)中选定蛋白质的肽段进行绝对含量测定时,相对标准偏差小于20%,准确度较高,说明该方法可用于复杂生物样本中蛋白质的绝对定量。更重要的是所建方法不仅解决了细胞培养氨基酸稳定同位素标记(SILAC)技术的重标试剂价格昂贵的问题,也为定量蛋白质组学提供了一种新的方法。     

用生物质谱方法研究抗肿瘤双β-咔啉与DNA及核苷酸的非共价结合

利用电喷雾傅里叶变换离子回旋共振质谱研究一系列双β-咔啉化合物与DNA的非共价结合. 发现化合物1—5与5种不同序列的12-mer双链DNA均有明显的非共价结合, 并且有两个β-咔啉环之间连接碳链的长度对此类化合物与双链DNA的非共价结合活性有明显影响. 同时对此类化合物对于DNA非共价结合的序列选择性进行了讨论. 另外还利用电喷雾离子阱质谱研究了双β-咔啉化合物2和4与4种单核苷酸的非共价结合.     

基于电喷雾电离质谱(ESI-MS)的丙酮稳定同位素标记对N-糖链的相对定量分析方法的研究

建立了一种基于电喷雾电离质谱的丙酮稳定同位素标记对N-糖链进行相对定量的研究方法. 与传统的PNGase F酶水解N-糖链的方法不同,采用非特异性蛋白酶Pronase E对N-糖蛋白进行处理,使N-糖蛋白被酶解为带有一个氨基酸的糖氨酸（Glycan-Asn）,为N-糖链引入了一个氨基活性基团,然后用丙酮对氨基进行标记. 用d₀/d₆丙酮对Ribo B标准糖蛋白的Pronase E酶解产物进行标记,考察了4对d₀/d₆丙酮标记的Glycan-Asn（Man₅～Man₈-Asn）在电喷雾电离质谱中的线性、动态范围以及重现性. 结果表明,在10倍动态范围内,相对定量方法有良好的线性关系（R=0.9981）和重现性（CV<8.7%）. 并将建立的方法应用于不同含量的鸡卵清白蛋白中,进一步验证了该方法的可行性. 研究结果表明,该方法能准确分析样品中N-糖链的含量,对不同样品中N-糖链进行相对定量. 该方法成本低廉,后处理方法简单方便,适于微量样品通量化分析,对差异糖组的研究有一定的意义.     

Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level

The post-genomic era and increased demands for broad proteome measurements have greatly increased the needs for protein identification. We describe a strategy that uses accurate mass measurements and partial amino acid content information to unambiguously identify intact proteins, and show its initial application to the proteomes of Escherichia coli and Saccharomyces cerevisiae. Proteins were extracted from the organisms grown in minimal medium or minimal medium to which isotopically labeled leucine (Leu-D(10)) had been added. The two protein extracts were mixed and analyzed by capillary isoelectric focusing (CIEF) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR). The incorporation of the isotopically labeled residue has no effect on the CIEF separation of proteins, and both isotopically labeled and unlabeled versions of specific proteins are observed within the same mass spectrum. The difference in the mass of the unlabeled and labeled proteins is used to determine the number of Leu residues present in a particular protein. Proteins can then often be unambiguously identified based on their accurately determined molecular mass and the additional constraint provided by number of Leu residues. The identities of proteins were further confirmed by repeating CIEF/FTICR measurements with samples that contain other isotopically labeled amino acid residues (e.g. His, Arg, Ile, Phe, Lys). A theoretical study of the amino acid composition (for a difference in the amino acid sequence) showed the constraints needed in order to identify the protein unambiguously. Additionally, the mass differences between the predicted and the experimental accurate mass measurement provide insights into the nature of simple post-translational modifications.     

Mass-spectrometric analysis of complex volatile and nonvolatile crude oil components: a challenge

Crude oil analysis has long been an inspiration for the development of analytical techniques. Especially mass spectrometry has flourished as a result of the challenge these extremely complex problems offer. Here an overview of different analytical methods is presented that shows different ways to analyze volatile and nonvolatile crude oil components. Focus has been placed on the use of mass spectrometry and especially the new developments that have been introduced using the emerging technique of Fourier transform ion cyclotron resonance mass spectrometry. These studies are examples of how far the development of analytical methods has come for the task of studying such complex problems.     

Molecular level comparison of water extractives of maple and oak with negative and positive ion ESI FT‐ICR mass spectrometry

Soluble extractives in wood function to protect living trees from destructive agents and also contribute to wood color and fragrance. Some extractive components have biological activities with medical applications. They also play important roles in wood processing and related applications. To increase the knowledge of wood chemistry, maple and oak were extracted by water. Ultraviolet/visible (UV/vis) spectroscopy indicated the presence of a phenolic compound, resorcinol, in maple extractives having higher molecular mass and more aromatic components than oak extractives. Negative and positive electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT‐ICR‐MS) identified thousands of formulas in the two samples in the m/z range of 200 to 800. They mainly fall into the lignin‐like, carbohydrate‐like, and tannin‐like compound categories. The top 25 peaks (ie, formulas) with the highest relative magnitude in negative ESI represented nearly 50% of the summed total spectral magnitude of all formulas assigned in the maple and oak extractives. Furthermore, the base peak (ie, most abundant peak) accounted for about 14% of the total abundance in each wood sample. Literature comparisons identified 17 of 20 formulas in the top five peaks of the four spectra as specific bioactive compounds in trees and other plants, implying the potential to explore utilization of maple and oak extractives for functional and medicinal applications. The various profiling of the top 25 peaks from the two samples also suggested the possible application of FT‐ICR‐MS for detecting chemical markers useful in profiling and identification of wood types and sources.     

基质与样品的相互作用对于傅立叶变换离子回旋共振质谱测定低分子量多肽的影响

通过比较两种极性差异较大的基质2,5-二羟基苯甲酸(DHB)和2’,6’-二羟基苯乙酮(DHAP)按不同比例混合时,AngiotensinⅡ的基质辅助激光解析电离-傅立叶变换离子回旋共振质谱(MALDI-FT/ICRMS)谱图的不同,并结合基质-AngiotensinⅡ在不同结晶方式下的共结晶和基质晶体的扫描电镜照片,发现基质为10μmol/L DHB和15μmol/L DHAP以体积比4:1组成的混合物时,基质结晶为致密的层状结构,而以薄层法与AngiotensinⅡ生成的共结晶,AngiotensinⅡ在基质晶体上面形成分散的柱状小晶体,此时得到的MALDI-FT/ICRMS质谱图优于干滴法。     

Qualitative and quantitative studies on chemical constituents of Ling-gui-zhu-gan decoction: In vitro and in vivo

Ling-gui-zhu-gan decoction has significant therapeutic effects in the treatment of diseases related to phlegm and fluid retention. In this study, we aimed to qualitatively characterize the chemical constituents of Ling-gui-zhu-gan decoction in vitro and in vivo by HPLC coupled to Fourier transform ion cyclotron resonance MS, and quantitively determine the contents of typical chemical constituents by HPLC method. As a result, a total of 75 chemical constituents were discovered including 37 flavonoids and their glycosides, 20 saponins, 9 sterols, 3 organic acids and their derivatives, 3 lactones, 2 coumarins, and 1 alcohol. Among them, 17 chemical constituents were specifically identified. Subsequently, an HPLC method was established for simultaneous determination of seven chemical constituents. Finally, a total of 40 prototype components were initially detected by HPLC-MS method in the biological samples of rats after their water extract was orally administrated. Among them, 29, 27, 12, and 32 prototype components were detected in plasma, bile, urine, and feces, respectively. Moreover, 34 metabolites, including 16 phase II metabolites, were detected for the first time. In conclusion, this study lays the foundation for the identification of chemical components in vitro and in vivo and the elucidation of the potential pharmacodynamic components of Ling-gui-zhu-gan decoction.     

Identification of chemical components in Baidianling Capsule based on gas chromatography–mass spectrometry and high‐performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry

Baidianling Capsule, which is made from 16 Chinese herbs, has been widely used for treating vitiligo clinically. In this study, the sensitive and rapid method has been developed for the analysis of chemical components in Baidianling Capsule by gas chromatography–mass spectrometry in combination with retention indices and high‐performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry. Firstly, a total of 110 potential volatile compounds obtained from different extraction procedures including alkanes, alkenes, alkynes, ketones, ethers, aldehydes, alcohols, phenols, organic acids, esters, furans, pyrrole, acid amides, heterocycles, and oxides were detected from Baidianling Capsule by gas chromatography–mass spectrometry, of which 75 were identified by mass spectrometry in combination with the retention index. Then, a total of 124 components were tentatively identified by high‐performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry. Fifteen constituents from Baidianling Capsule were accurately identified by comparing the retention times with those of reference compounds, others were identified by comparing the retention times and mass spectrometry data, as well as retrieving the reference literature. This study provides a practical strategy for rapidly screening and identifying the multiple constituents of a complex traditional Chinese medicine.     

Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS) is the best MS technology for obtaining exact mass measurements owing to its great resolution and accuracy, and several outstanding FT-ICR/MS-based metabolomics approaches have been reported. A reliable annotation scheme is needed to deal with direct-infusion FT-ICR/MS metabolic profiling. Correlation analyses can help us not only uncover relations between the ions but also annotate the ions originated from identical metabolites (metabolite derivative ions). In the present study, we propose a procedure for metabolite annotation on direct-infusion FT-ICR/MS by taking into consideration the classification of metabolite-derived ions using correlation analyses. Integrated analysis based on information of isotope relations, fragmentation patterns by MS/MS analysis, co-occurring metabolites, and database searches (KNApSAcK and KEGG) can make it possible to annotate ions as metabolites and estimate cellular conditions based on metabolite composition. A total of 220 detected ions were classified into 174 metabolite derivative groups and 72 ions were assigned to candidate metabolites in the present work. Finally, metabolic profiling has been able to distinguish between the growth stages with the aid of PCA. The constructed model using PLS regression for OD₆₀₀ values as a function of metabolic profiles is very useful for identifying to what degree the ions contribute to the growth stages. Ten phospholipids which largely influence the constructed model are highly abundant in the cells. Our analyses reveal that global modification of those phospholipids occurs as E. coli enters the stationary phase. Thus, the integrated approach involving correlation analyses, metabolic profiling, and database searching is efficient for high-throughput metabolomics. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Studies on chemical constituents of Flos Puerariae-Semen Hoveniae medicine pair by HPLC and Fourier transform ion cyclotron resonance mass spectrometry

Alcoholic liver disease is currently the most clinically concerning liver disease, which occurs from chronic alcohol abuse. Flos Puerariae and Semen Hoveniae have been used to treat alcohol drinking excessively for thousands of years in China. In this study, the ethanol extract of the medicine pair was qualitatively and quantitatively analyzed by high-performance liquid chromatography and Fourier transform ion cyclotron resonance mass spectrometry. First, the high-performance liquid chromatography fingerprint was established to obtain the overall chromatographic data of its chemical constituents. Next, high-performance liquid chromatography-mass spectrometry was applied to identify its chemical constituents. Then, the characteristic constituents were simultaneously quantified by high-performance liquid chromatography. In addition, the chemical constituents that were absorbed into rat plasma were identified by high-performance liquid chromatography-mass spectrometry. As a result, a total of 48 chemical constituents in the medicine pair were detected and identified in vitro. Meanwhile, the content of seven representative constituents, including dihydromyricetin, glycitin, genistin, tectoridin, glycitein, genistein, and tectorigenin were simultaneously determined. Furthermore, a total of 19 chemical constituents were detected in rat plasma after oral administration. In short, the chemical constituents of the medicine pair were initially investigated in this study, which will lay the foundation for the discovery of its pharmacodynamic substances in further works.