基于强阳离子交换色谱分离的磷酸化肽段富集策略

为了在短时间内获得相对含量高的磷酸化肽段,以标准磷酸化蛋白质为模型对强阳离子交换色谱（SCX）分离磷酸化肽段体系的缓冲溶液和梯度设置进行了研究,并用酵母酶切肽段混合物考察了该路线在较复杂的样品中的应用。实验结果表明优化后的体系能够在30 min内分离出磷酸肽段,而且非磷酸化肽段的干扰很少,这样便相对提高了磷酸化肽段在质谱仪中的响应强度,重要的是该体系可以对复杂样品进行很好的分离。这说明SCX用于规模化磷酸化肽段富集的策略是可行的。本研究为磷酸化蛋白质组学规模化分析提供了实用技术。     

等电聚焦分离与18O稳定同位素标记联用的磷酸化蛋白质组学定量方法研究

磷酸化蛋白质组学定量分析,要对磷酸化修饰富集技术和定量技术进行研究。基于此,本研究采用18O稳定同位素标记技术对胰蛋白酶酶解肽段混合物进行标记,并对其标记时间和标记后胰蛋白酶的变性条件进行优化。结果表明:在pH=4～5的KH2PO4缓冲体系中,37℃,标记反应持续19～24h,除了C-端肽之外,几乎所有的肽段都可达到100%标记;采用TCEP可以有效地抑制16O-18O回标现象。建立了与18O标记技术兼容性良好的IPG-IEF技术对磷酸化肽段进行选择性富集,富集后共从HepG2细胞中鉴定到491个磷酸化位点、362个磷酸化肽段和356个磷酸化蛋白,表明IPG-IEF在大规模磷酸化肽段分离富集中是有效的;最后与高准确度高灵敏度高分辨率的LTQ-FTICR质谱仪联用,建立了基于18O-IPG-IEF-LTQ-FTICR的磷酸化蛋白质组定量技术。实验结果表明,该技术可以实现磷酸化肽段的有效定性和定量。本研究为磷酸化蛋白质组学定量研究提供了实用技术。     

新型等点聚焦系统用于蛋白质组样本的预分离方法研究

对蛋白质或多肽的高效分离,将有利于降低肽段信号之间的干扰,保证规模化的蛋白质组学深度覆盖鉴定,并提高定量蛋白质组分析的准确性。本研究采用一种新型的等电聚焦预分离系统(OFFGEL),考察系统对293T细胞在蛋白质与肽段水平的分级分离效果,在OFFGEL系统中聚焦后的蛋白质或肽段可以从溶液中直接回收,与下游的LC-MS/MS肽段鉴定流程兼容。实验结果表明,肽段的分离效果明显优于蛋白质的分离,分级分离后各馏分对应的等电点位置与肽段的理论等电点分布高度一致,每个馏分中单独鉴定的肽段比例超过90%,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293T细胞中实现6727个蛋白质的规模化鉴定,表明该系统在复杂体系蛋白质组研究中的应用潜力。     

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。     

基于两相预柱的在线二维分离系统用于人肝组织中磷酸肽的规模化鉴定

将C18反相(RP)填充柱和磷酸基强阳离子交换(SCX)整体柱集成于一体的RP - SCX两相预柱,成功用于RPLC - MS/MS系统的自动进样和SCX分级,完成了磷酸肽在线多维分离平台的构建,可以减少样品的损失,极大地提高了系统的集成化水平和检测灵敏度.对人肝组织酶解液富集的磷酸肽进行规模化鉴定,在假阳率小于1％的情况下,共鉴定到3082条非重复的磷酸化肽段、3056个磷酸化位点和1332个磷酸化蛋白.对所鉴定到的磷酸化蛋白进行了功能分类和激酶分析.该实验结果对于了解蛋白质磷酸化在肝脏组织中发挥的生理学作用具有重要意义.     

无孔单分散亲水性强阳离子交换固定相的制备及其在蛋白质快速分离中的应用研究

采用分散聚合法制备小颗粒种子及“一步种子溶胀聚合”法成功地制备了粒径为3.0 μm的无孔单分散亲水性交联聚甲基丙烯酸环氧丙酯树脂,其表面经水解、环氧化、再水解后与氯磺酸反应,制备了一种新型的强阳离子交换色谱填料（SCX）。详细考察了该填料对标准蛋白质的分离性能及流动相中盐的种类、有机溶剂、流速等对蛋白质保留的影响。实验结果表明,在流速为4 mL/min时,采用线性梯度洗脱,1.0 min内可快速分离4种标准蛋白质,蛋白质的保留符合阳离子交换色谱规律。将SCX应用于快速纯化鸡蛋清中的溶菌酶和猪心中的细胞色素-C,取得了较好的效果。     

基于共价色谱分离的含半胱氨酸肽段富集策略

多维色谱分离、串联质谱分析技术已在蛋白质组研究中得到广泛应用。然而生物样品的蛋白质以及全酶切肽段具有高度的复杂性,这严重干扰了蛋白质高通量、规模化的分析。通过标签肽段富集进行样品预分离可以降低体系的复杂程度。本文建立了一种基于共价色谱技术选择性分离富集含半胱氨酸肽的方法,从而降低了样品体系的复杂程度。首先以牛血清白蛋白(BSA)的酶切肽段为模型,对富集条件进行了优化和考察,并在此基础上通过5种蛋白质酶切肽段混合物的富集对该方法进行了验证。结果证明此方法的重现性好,富集效率高,富集特异性好,能有效地富集鉴定含半胱氨酸肽段。所建立的方法在复杂体系的蛋白质组研究中具有广泛的应用前景,为复杂样品的蛋白质高通量、自动化、规模化鉴定和定量研究提供了实用技术。     

磺化修饰结合离子交换色谱和生物质谱富集鉴定含组氨酸肽段

通过在肽段的N端引入磺酸基,从而使含组氨酸的肽段与其他肽段在pH<3.0的条件下产生电荷差异,建立了一种基于强阳离子交换色谱(SCX)结合生物质谱富集鉴定含组氨酸肽段的方法,并以含有组氨酸的标准蛋白质为模型,进行了方法学考察。结果表明,经N端磺酸化后,含组氨酸的肽段能有效地被阳离子交换色谱富集,且在肽的N端引入磺酸基促进了肽的裂解,使之产生简单而信息丰富的二级质谱图,从而得到完美的质谱鉴定结果。这说明磺化修饰结合强阳离子交换色谱用于含组氨酸肽段的富集鉴定是可行的,且具有在蛋白质组研究中应用的潜力。     

纳米材料在蛋白磷酸化分析中的应用研究

蛋白质磷酸化修饰是一种重要的蛋白质翻译后修饰,在细胞代谢过程中发挥着重要作用。当蛋白质的正常磷酸化调节发生异常时,会导致癌症、糖尿病、心脏病等各种疾病的发生。因此,蛋白磷酸化分析对于疾病的早期快速诊断、药物筛选和治疗等方面具有重大的意义。由于蛋白质磷酸化过程是动态的,并且磷酸化肽段或蛋白在生物样品中的含量较低,因此高灵敏的蛋白磷酸化分析面临着巨大的挑战。该文依据在检测过程中,选择性识别或捕获磷酸化的肽段或蛋白的主要机理,综述了近几年纳米材料对磷酸化肽段的富集和信号放大作用在蛋白磷酸化分析中的研究进展,并对其未来研究方向进行了展望。     

基于TMT10-plex等量标记结合SMOAC富集磷酸肽的定量磷酸化蛋白质组性能评价

探索并建立了一种快速、 简便且高通量定量磷酸化蛋白质组的策略, 即采用连续互补的磷酸化富集方法SMOAC(Sequential enrichment of metal oxide affinity chromatography)结合TMT(Tandem mass tag)标记技术定量磷酸化蛋白质组学. 以3例经紫草素处理的及3例正常的人肝癌 HepG2 细胞为实验材料, 经Trypsin酶解后的肽段用TMT10-plex试剂进行等量标记, 标记肽段先经TiO₂富集, 收集包含磷酸化肽段的洗脱液, 接着用次氮基三醋酸铁(Fe-NTA)对TiO₂的流穿液和清洗液进行二次富集, 再次收集包含磷酸化肽段的洗脱液. 整个实验流程做2组, 对其中一组的2次洗脱液分别分析, 另一组的2次洗脱液合并分析. 在SMOAC的2次洗脱液合并分析中鉴定到4263个磷酸化蛋白上超过13000条磷酸化肽, 富集特异性>97%, 其中被定量的磷酸化蛋白为3848个, 占总鉴定量的90%以上. 研究结果表明, SMOAC 能够有效提高磷酸化肽段的鉴定效率, 且能与TMT等量标记试剂结合, 实现对少量蛋白样品的磷酸化蛋白定量分析.     

pI-based phosphopeptide enrichment combined with nanoESI-MS

IEF is introduced as a new principle for enrichment and separation of phosphopeptides as obtained after digestion of phosphoproteins by trypsin. Tryptic peptides and phosphopeptides exhibit pI values, which overlap in the range of about 4-6. However, after methyl esterification of all carboxyl functions, the pI values of tryptic peptides and phosphopeptides regroup in discrete clusters. In addition, mono- and diphosphorylated peptides show different but very homogeneous pI values, with variations when internal Arg, Lys, or His residues are present. Experimentally, this new concept was applied for separation of model peptides on IPG strips pH 3-10 as used in the first dimension of 2-DE. After IEF of methyl-esterified peptides, the IPG strip was cut into pieces followed by peptide extraction, desalting and MS analysis by nanoESI-MS. Phosphopeptides were found to focus in good agreement with their calculated pI values. This analytical strategy showed a resolution of about 0.2 pI units, and thus turned out to be capable of detecting minor differences in pI values, such as those occurring between pSer, pThr and pTyr residues. Using IPG strips with a pI range of 3-10, methyl esterified nonphosphorylated tryptic peptides are concentrated in the basic part of the IPG strip or even leave the strip. Thus, efficient enrichment of phosphopeptides and their subfractionation according to pI is obtained in one step. Minor hydrolytic side reactions including deamidation of Asn and partial hydrolysis of methyl esters are observed. The results show that IEF opens attractive avenues for the further advancement of analytical phosphoproteomics.     

Two-dimensional gel electrophoresis of platelet polypeptides with immobilized pH gradients in capillary tubes

Two-dimensional electrophoresis (2-DE) with immobilized pH gradient (IPG) gels in capillary tubes was used in the first-dimensional isoelectric focusing (IEF) for the separation of human platelet polypeptides. Two types of IPG tube gels, pH ranges 4-8 and 7-10, containing 8 M urea, 1% Nonidet P-40 and 0.1% pH 3.5-10 Ampholine carrier ampholytes (CA) were prepared by a simple method not requiring special equipment. The addition of CA to both gel and sample solutions was essential in the tube gel IPG system. Proteins were visualized by a modification of Wray's silver-staining technique. The degree of resolution and the number of spots observed on an IPG 2-DE gel with pH 4-8 were comparable with those obtained with O'Farrell's high-resolution 2-DE. Approximately 200 basic polypeptides, which are difficult to separate by conventional CA-based IEF 2-DE or the non-equilibrium pH gradient system, were well resolved by 2-DE with a pH 7-10 IPG tube gel in the first-dimension. The gel patterns with either pH gradient 4-8 or 7-10 were highly reproducible among gels prepared and run simultaneously. These results demonstrated the potential and usefulness of the 2-DE system with IPG gels in capillary tubes.     

Phosphopeptide enrichment by IEF

In our efforts to improve the identification of phosphopeptides by MS we have used peptide IEF on IPG strips. Phosphopeptides derived from trypsin digests of single proteins as well as complex cellular protein mixtures can be enriched by IEF and recovered in excellent yields at the acidic end of an IPG strip. IPG peptide fractionation in combination with MS/MS analysis has allowed us to identify phosphopeptides from tryptic digests of a cellular protein extract.     

Agarose isoelectric focusing can improve resolution of membrane proteins in the two-dimensional electrophoresis of bacterial proteins

2-D separation of bacterial membrane proteins is still difficult despite using high-resolution IPG-IEF/SDS-PAGE. We were searching for alternative methods to avoid typical problems such as precipitation, low solubility, and aggregation of membrane proteins in the 1-D separation with IPG-IEF. Blue native electrophoresis (BNE) and agarose IEF (A-IEF) were tested for their separation capacity and their capability of replacing IPG-IEF in the first dimension. SDS-PAGE was chosen for the second dimension on account of its outstanding resolution. We could confirm that only A-IEF was a useful replacement for the IPG-IEF in the first dimension resulting in 2-D protein distributions with additional membrane protein spots not being found after IPG-IEF/SDS-PAGE. A second interesting result was that the agarose IEF mediates the possibility of separation of membrane proteins in a partially native state in the first dimension. This native A-IEF resulted in drastically changed spot patterns with an acidic shift of nearly all spots and divergent distribution of proteins compared to non-native A-IEF and IPG-IEF. We found out that native and non-native A-IEF are powerful tools to supplement IPG-IEF/SDS-PAGE.     

Highly efficient enrichment of phosphopeptides by magnetic nanoparticles coated with zirconium phosphonate for phosphoproteome analysis

The location of phosphorylation plays a vital role for the elucidation of biological processes. The challenge of low stoichiometry of phosphoproteins and signal suppression of phosphopeptides by nonphosphopeptides in mass spectrometry (MS) analysis makes the selective enrichment of phosphopeptides prior to MS analysis necessary. Besides the immobilized metal affinity chromatography (IMAC) method, some affinity methods based on nanoparticles displayed a higher enrichment efficiency for phosphopeptides such as Fe(3)O(4)/TiO2 and Fe(3)O(4)/ZrO(2) nanoparticles. To further improve the selectivity and compatibility of the affinity methods, a novel strategy based on magnetic nanoparticles coated with zirconium phosphonate for the enrichment of phosphopeptides has been developed in this study. Under optimized experimental conditions, 1 x 10(-9) M phosphopeptides in 50 microL tryptic digest of beta-casein could be enriched and identified successfully. Reliable results were also obtained for 1 x 10(-8) M phosphopeptides in 50 microL tryptic digest of beta-casein in the presence of nonphosphopeptides from a tryptic digest of bovine serum albumin (BSA) over 20 times in concentration. The performance of nanoparticles for use in a real sample was further demonstrated by employing the strong cation-exchange chromatography (SCX) fraction of a tryptic digest of a protein extract from Chang liver cells as a model sample. Experimental results show that the nanoparticles can be easily and effectively used for enrichment of phosphopeptides in low concentration. Most importantly, our approach is more compatible with commonly used SCX strategies than Fe(3+)-IMAC. The proposed method thus has great potential for future studies of large-scale phosphoproteomes.     

Isoelectric focusing in immobilized pH gradients with carrier ampholytes added for high-resolution phenotyping of bovine beta-lactoglobulins: characterization of a new genetic variant

The genetic variants of bovine beta-lactoglobulin (beta-lg) from the "Murnau-Werdenfelser" breed were analyzed in three different isoelectric focusing (IEF) systems. While carrier ampholyte IEF with a pH gradient of 0.2 pH/cm did not resolve the new variant W from the B variant and IEF in immobobilized pH gradients (IPG) with 0.1 pH/cm only partially resolved it, adequate separation was achieved with IPG-IEF in a pH 5.25-pH 5.7 gradient, in presence of 0.8 % w/v carrier ampholytes, both over a 10 and 17 cm separation distance. Apparent isoelectric points (pI's) and genetic frequencies (f) were as follows: beta-lg A, pI = 5.370, f = 0.364; beta-lg B, pI = 5.485, f = 0.480; beta-lg W, pI = 5.492, f = 0.076; and beta-lg D, pI = 5.610, f = 0.080. The small difference of delta pI = 0.007 between beta-lg B and beta-lg W respectively, seems to originate from a "silent" substitution of neutral amino acid residues as compared to the larger delta pI's of the other genetic variants of beta-lg, which result from substitution of charged amino acids.     

蛋白质组学中磷酸化肽的常用富集方法

磷酸化作用是最重要的蛋白质翻译后修饰方式之一,它是蛋白质组学的一个重要分支,在细胞识别、细胞信息传递、基因表达和新陈代谢等方面发挥着重要作用。采用适当方法对磷酸化肽进行分析有助于我们更好地了解生理病理机制。但是直接进行质谱分析时磷酸化肽的信号强度会受到无机盐以及大量非磷酸化肽的抑制,选择性差。为解决这一难题,在质谱分析前要对磷酸化肽进行选择性富集。本文回顾了几种常用的磷酸化肽富集方法,介绍了每种方法的发展状况和常用材料,其中包括固定金属离子亲和色谱法、金属氧化物富集法、强阴阳离子交换色谱法和MALDI靶板富集法。最后总结了各种富集方法的优缺点,对有效的磷酸化肽富集策略进行了前景展望。     

Fe3O4@Al2O3 magnetic core-shell microspheres for rapid and highly specific capture of phosphopeptides with mass spectrometry analysis

Selective detection of phosphopeptides from complex biological samples is a challenging and highly relevant task in many proteomics applications. In this study, a novel phosphopeptide enrichment approach based on the strong interaction of Fe(3)O(4)@Al(2)O(3) magnetic core-shell microspheres with phosphopeptides has been developed. With a well-defined core-shell structure, the Fe(3)O(4)@Al(2)O(3) magnetic core-shell microspheres not only have a shell of aluminum oxide, giving them a high-trapping capacity for the phosphopeptides, but also have magnetic property that enables easy isolation by positioning an external magnetic field. The prepared Fe(3)O(4)@Al(2)O(3) magnetic core-shell microspheres have been successfully applied to the enrichment of phosphopeptides from the tryptic digest of standard phosphoproteins beta-casein and ovalbumin. The excellent selectivity of this approach was demonstrated by analyzing phosphopeptides in the digest mixture of beta-casein and bovine serum albumin with molar ratio of 1:50 as well as tryptic digest product of casein and five protein mixtures. The results also proved a stronger selective ability of Fe(3)O(4)@Al(2)O(3) magnetic core-shell microspheres over Fe(3+)-immobilized magnetic silica microspheres, commercial Fe(3+)-IMAC (immobilized metal affinity chromatography) resin, and TiO(2) beads. Finally, the Al(2)O(3) coated Fe(3)O(4) microspheres were successfully utilized for enrichment of phosphopeptides from digestion products of rat liver extract. These results show that Fe(3)O(4)@Al(2)O(3) magnetic core-shell microspheres are very good materials for rapid and selective separation and enrichment of phosphopeptides.     

磷酸化肽段分离富集方法研究进展

目前磷酸化肽段鉴定主要依赖于质谱技术,但磷酸化肽段的低丰度性以及来自非磷酸化肽段的干扰等因素,影响质谱的分析与鉴定。因此质谱分析前磷酸化肽段的富集,是深入研究磷酸化蛋白质组学的先决条件。该文介绍了磷酸化蛋白质组学中传统的以及新建立的一些磷酸化肽段分离富集方法的原理及优缺点,这些方法包括固相金属离子亲和色谱法(IMAC)、金属氧化亲和色谱法(MOAC)、强阳/阴离子交换色谱法(SCX/SAX)、亲水相互作用色谱法(HILIC)、静电排斥亲水相互作用色谱法(ERLIC)、化学衍生法、MALDI靶盘富集法以及多种富集方法相结合。