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。     

基于荧光偏振的高灵敏度蛋白激酶活性分析

利用TiO₂纳米棒与磷酸化肽的特异性相互作用,基于荧光偏振检测,建立了快速、简便的高灵敏度蛋白激酶活性分析方法. 在蛋白激酶催化作用下,荧光标记的肽底物被磷酸化,磷酸化的荧光肽通过磷酸基团特异性结合在TiO₂纳米棒表面,从而使底物肽上标记的荧光分子的旋转速率发生改变,通过对荧光偏振度进行测量,可实现蛋白激酶活性的定量检测,该方法对蛋白激酶A(PKA)的检出限可达0.0004 U·μL^-1. 此外,该方法还成功用于PKA抑制剂H-89的检测,在基于蛋白激酶抑制剂的靶向药物筛选方面具有很好的应用前景.     

介孔氧化铁材料快速、高效富集分离磷酸化肽段和蛋白的新方法研究

以0.1μmol/Lβ-casein磷酸化蛋白酶解液为对象,利用在酸性条件下对PO43-能够特异性吸附的氧化铁材料为新载体,对介孔氧化铁材料富集分离磷酸化肽段的孵育液酸含量、孵育液有机溶剂含量和洗脱液选择的条件进行了优化,结果表明:室温条件下,在含有0.1%乙酸和30%乙腈的孵育液中孵育5min后,经1mol/LNH3.H2O溶液的洗脱,介孔氧化铁可有效地将磷酸化肽段从蛋白酶解液中富集分离。本方法也可以选择性地提取α-casein磷酸化蛋白,实现了简单、快速、高效的磷酸化肽段和蛋白的富集分离。同时,通过MALDI-TOF串级质谱分析,成功地完成了在优化条件下分离出的磷酸化肽段磷酸位点的鉴定。     

固定化金属离子亲和发光二氧化硅纳米粒子的制备及其用于磷酸化蛋白免疫印迹标记

发展了一种能够识别磷酸化蛋白的固定化金属离子亲和发光二氧化硅纳米粒子用于免疫印迹(Western Blot)磷酸化蛋白的标记。首先通过反相微乳液Stöber方法合成了掺杂异硫氰酸荧光素硅烷化衍生物的发光二氧化硅(FITC@SiO₂)球形纳米粒子,粒子平均粒径为60 nm。然后通过共聚反应在FITC@SiO₂纳米粒子表面生成一层聚合物用于保护纳米粒子,并引入N,N-(双羧甲基)-L-赖氨酸功能基团用于螯合金属离子,从而实现固定化金属离子亲和作用。以α-酪蛋白作为实验模型,用高效液相色谱-质谱研究了螯合不同金属离子的发光纳米粒子对磷酸化蛋白的识别作用。结果表明,螯合了Ti⁴⁺金属离子的发光二氧化硅FITC@SiO₂纳米粒子对α-酪蛋白酶解液中的磷酸化肽段的富集作用最强。利用这种发光二氧化硅FITC@SiO₂纳米粒子对磷酸化肽段的特异性识别性能,可用于Western Blot实验中标记磷酸化蛋白的条带。结果显示,α-酪蛋白的电泳条带可以被亲和发光二氧化硅FITC@SiO₂纳米粒子标记,而作为对照的牛血清白蛋白则没有被标记。     

基于亲和色谱的肺癌细胞磷酸化蛋白质组研究及其应用

磷酸化是蛋白质翻译后修饰的重要形式之一,其异常往往会导致细胞内信号通路的紊乱和疾病的发生。固定化金属离子亲和色谱(IMAC)是磷酸化肽段的高效富集技术,在磷酸化蛋白质组研究方面应用广泛。该研究以金属钛离子(Ti⁴⁺)螯合IMAC材料(Ti⁴⁺-IMAC)为载体,进行磷酸化肽段富集。比较了10 μm Ti⁴⁺-IMAC通过振荡法和固相萃取法(SPE)富集磷酸肽的效果,发现振荡法可以富集到更多的磷酸肽;对比了两种尺寸(10 μm和30 μm)Ti⁴⁺-IMAC在磷酸化肽段富集中的差异,发现小尺寸材料富集效果更佳。进一步采用优化的策略比较了不同转移能力肺癌细胞的磷酸化蛋白质组,免标记定量蛋白质组学结果表明,优化的Ti⁴⁺-IMAC方法可以从正常的肺成纤维细胞MRC5、低转移肺癌细胞95C和高转移肺癌细胞95D中分别鉴定到510、863和1108种磷酸化蛋白质,其中317种为3组所共有。该研究共鉴定到1268种磷酸化蛋白质上的7560个磷酸化位点,其中1130个为差异磷酸化位点,文献报道显示部分异常表达的激酶与癌症转移密切相关。通过生信对比分析发现,异常表达的磷酸化蛋白质主要与细胞侵袭、迁移和死亡等细胞迁移方面的功能有关。通过优化磷酸化肽富集策略,初步阐明了磷酸化蛋白质网络的异常与肺癌转移之间的相关性,该方法有望用于肺癌进展相关的磷酸化位点、磷酸化蛋白质及其信号通路研究。     

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。     

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。     

黄腐酸的选择性甲基化

用1-甲基-3-对甲苯基三氮烯(TMT)作为一种烷基化试剂,在常温与无催化剂的条件下对黄腐酸及一些羟基苯羧酸与酚类模型化合物进行甲基化.实验结果证明,TMT能定量地和选择性地与pH<7的酸性基团(主要是羧基)起反应.对用TMT甲基化的与用CH₂N₂和(CH₃)₂SO₄甲基化的黄腐酸的元素组成、甲氧基含量、分子量以及它们的红外光谱和核磁共振谱进行了鉴别与比较.这些结果表明,TMT甲基化能改进黄腐酸在有机溶剂中的溶解度,而不改变其基本结构.此外,对TMT甲基化黄腐酸中新出现的一条1510～1530cm^-1红外吸收带作了解释.     

蛋白质组衍生肽段文库用于鉴定酪蛋白激酶2的底物模体

模体是蛋白质二级结构上的一种特征序列,激酶底物通常具有一类特征性的模体,识别底物模体对鉴定激酶底物具有重要意义。为了快速鉴定激酶底物模体,将全细胞蛋白质酶解液作为肽段文库的来源,采用碱性磷酸酶去除肽段的固有磷酸化后构建了用于筛选激酶底物模体的肽段文库。该肽段文库是大量非磷酸化肽段的混合物,将此混合肽段与酪蛋白激酶2和三磷酸腺苷作用30 min后,通过固定化金属离子亲和色谱法富集磷酸化肽段,采用反相液相色谱-串联质谱分析,成功地鉴定到472条非冗余底物肽段,包含451个非冗余磷酸化位点,并由此得到底物模体S/T-D/E-x-D/E。该法能够快速准确地筛选出激酶底物模体,对研究激酶-底物识别以及信号转导过程具有重要意义。     

2D/3D ZnIn2S4/TiO2复合物的原位构筑及其提高的光催化性能

通过高温煅烧和油浴的方法构筑二维/三维(2D/3D) ZnIn₂S₄/TiO₂异质结, 应用于光催化降解罗丹明B (RhB)和四环素(TC), 来研究异质结的构筑对TiO₂可见光响应范围和光生载流子对分离效率的影响. 结果表明, TiO₂维持了MOFs的形貌, 显示窄的可见光响应范围和高的光生电荷复合率, 与ZnIn₂S₄纳米片复合后, TiO₂的比表面积增大, 光催化活性位点增多. 带隙宽度也由TiO₂的3.23 eV减小到ZnIn₂S₄/TiO₂-II的2.52 eV, 从而获得了更宽的可见光响应范围. 能带结构表明ZnIn₂S₄/TiO₂是type II型异质结, 提高了光生载流子对的分离与转移效率. 在可见光照射下, ZnIn₂S₄/TiO₂-II显示了最高的RhB光催化降解效率(93%), 分别是TiO₂和ZnIn₂S₄的18和2倍. 同时, ZnIn₂S₄/TiO₂-II也显示出比TiO₂和ZnIn₂S₄更高的TC降解效率(90%). 循环实验表明ZnIn₂S₄/TiO₂-II能保持良好的稳定性, 经5次循环实验后仍能降解83%的RhB. 研究表明基于MOFs衍生的TiO₂构筑2D/3D ZnIn₂S₄/TiO₂异质结是提高TiO₂光催化性能的一条有效途径.     

Evaluation of the impact of some experimental procedures on different phosphopeptide enrichment techniques

The complete characterization of phosphorylated proteins requires an efficient procedure for the enrichment of phosphopeptides from amongst a complicated peptide mixture. The sensitivity of the traditional immobilized metal affinity chromatography (IMAC) approach is severely affected by various buffers, detergents and other reagents normally utilized in biochemical and cell biological procedures, and thus pre-purification steps such as reversed-phase chromatography is required prior to phosphopeptide enrichment. Here we evaluate the use of different 'non-phosphopeptide-excluding compounds' in the loading buffer for titanium dioxide (TiO(2)) chromatography and show that TiO(2) is more robust and tolerant towards many reagents, including salts, detergents and other low molecular mass molecules, than conventional IMAC. In addition, we show that the inclusion of various detergents can enhance the efficiency of this enrichment method, as phosphopeptides that otherwise adhere to plastic surfaces can be efficiently solubilized and subsequently purified. The TiO(2) chromatography technique is also compared to zirconium dioxide chromatography for phosphopeptide enrichment.     

Enrichment and analysis of phosphopeptides under different experimental conditions using titanium dioxide affinity chromatography and mass spectrometry

Titanium dioxide metal oxide affinity chromatography (TiO₂‐MOAC) is widely regarded as being more selective than immobilized metal‐ion affinity chromatography (IMAC) for phosphopeptide enrichment. However, the widespread application of TiO₂‐MOAC to biological samples is hampered by conflicting reports as to which experimental conditions are optimal. We have evaluated the performance of TiO₂‐MOAC under a wide range of loading and elution conditions. Loading and stringent washing of peptides with strongly acidic solutions ensured highly selective enrichment for phosphopeptides, with minimal carryover of non‐phosphorylated peptides. Contrary to previous reports, the addition of glycolic acid to the loading solution was found to reduce specificity towards phosphopeptides. Base elution in ammonium hydroxide or ammonium phosphate provided optimal specificity and recovery of phosphorylated peptides. In contrast, elution with phosphoric acid gave incomplete recovery of phosphopeptides, whereas inclusion of 2,5‐dihydroxybenzoic acid in the eluant introduced a bias against the recovery of multiply phosphorylated peptides. TiO₂‐MOAC was also found to be intolerant of many reagents commonly used as phosphatase inhibitors during protein purification. However, TiO₂‐MOAC showed higher specificity than immobilized gallium (Ga³⁺), immobilized iron (Fe³⁺), or zirconium dioxide (ZrO₂) affinity chromatography for phosphopeptide enrichment. Matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) was more effective in detecting larger, multiply phosphorylated peptides than liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS), which was more efficient for smaller, singly phosphorylated peptides. Copyright © 2009 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.     

Phosphopeptide quantitation using amine-reactive isobaric tagging reagents and tandem mass spectrometry: application to proteins isolated by gel electrophoresis

Polyacrylamide gel electrophoresis is widely used for protein separation and it is frequently the final step in protein purification in biochemistry and proteomics. Using a commercially available amine-reactive isobaric tagging reagent (iTRAQ) and mass spectrometry we obtained reproducible, quantitative data from peptides derived by tryptic in-gel digestion of proteins and phosphoproteins. The protocol combines optimized reaction conditions, miniaturized peptide handling techniques and tandem mass spectrometry to quantify low- to sub-picomole amounts of (phospho)proteins that were isolated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Immobilized metal affinity chromatography (FeIII-IMAC) was efficient for removal of excess reagents and for enrichment of derivatized phosphopeptides prior to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis. Phosphopeptide abundance was determined by liquid chromatography/tandem mass (LC/MS/MS) using either MALDI time-of-flight/time-of-flight (TOF/TOF) MS/MS or electrospray ionization quadrupole time-of-flight (ESI-QTOF) MS/MS instruments. Chemically labeled isobaric phosphopeptides, differing only by the position of the phosphate group, were distinguished and characterized by LC/MS/MS based on their LC elution profile and distinct MS/MS spectra. We expect this quantitative mass spectrometry method to be suitable for systematic, comparative analysis of molecular variants of proteins isolated by gel electrophoresis.     

Development of core–shell structure Fe3O4@Ta2O5 microspheres for selective enrichment of phosphopeptides for mass spectrometry analysis

Protein phosphorylation is one of the most important post-translational modifications. Due to the dynamic nature and low stoichiometry of the protein phosphorylation, enrichment of phosphopeptides from proteolytic mixtures is often necessary prior to their characterization by mass spectrometry. Many metal oxides such as titanium dioxide and zirconium dioxide have been successfully applied to isolation and enrichment of phosphopeptides. Recently, niobium pentoxide was proved to have the ability for selective enrichment of phosphopeptides. Considering the proximity of tantalum to niobium, we supposed that Ta₂O₅ can be used as affinity probes for phosphopeptide enrichment. In the work, we synthesized Fe₃O₄@Ta₂O₅ magnetic microspheres with core–shell structure for selective enrichment of phosphopeptides. To demonstrate its ability for selective enrichment of phosphopeptides, we applied Fe₃O₄@Ta₂O₅ magnetic microspheres to isolation and enrichment of the phosphopeptides from tryptic digestion of standard proteins and real samples, and then the enriched peptides were analyzed by matrix-assisted laser desorption mass spectrometry analysis (MALDI-MS) or liquid chromatography coupled to electrospray ionization mass spectrometry (LC–ESI-MS). Experiment results demonstrate that Ta₂O₅ coated-magnetic microspheres show the excellent potential for selective enrichment of phosphopeptides.     

葡萄糖-6-磷酸功能化亲水磁探针：有效分离富集糖肽/磷酸肽的双用途亲和材料

在Fe₃O₄磁芯上通过逐层修饰构建了葡萄糖-6-磷酸(G6P)功能化亲水磁探针Fe₃O₄@PDA@TiO₂@G6P. 聚多巴胺(PDA)可以作为偶联连接剂进一步接枝二氧化钛(TiO₂); 接枝的TiO₂除作为G6P的锚定位点外, 还 可通过金属氧化物亲和层析技术有效富集磷酸肽; G6P的官能化赋予了纳米球高亲水性的表面, 并利用亲水作用液相色谱法实现了糖肽的捕捉. 实验结果表明, 探针对糖肽具有低的检出限(0.1 fmol/μL)、 高的选择性 [m(HRP)∶m(BSA)=1∶1000]、 良好的重复性(10次循环)和高的负载量(300 mg/g); 对磷酸肽具有低的检出限(0.02 fmol/μL)和高的选择性[n(β-casein)∶n(BSA)=1∶1000). 此外, 这种双用途亲和材料具有同时富集糖肽和磷酸肽的能力,可从人唾液中鉴定出34个糖肽和36个磷酸肽, 表明其在多种翻译后修饰的蛋白质组学分析中具有巨大的应用前景.     

Synthesis of BC@mTiO<Subscript>2</Subscript> hybrid nanofibers for highly efficient enrichment and detection of phosphopeptides

Along with advances in life science and clinical research, there has been an increasing interest in enrichment technologies for proteins with post-translational modifications. Here we report a new platform to enrich and detect phosphopeptides using the hybrid nanofibers synthesized from bacterial cellulose (BC). Hydrothermal reactions have successfully been employed to synthesize BC@mTiO₂ hybrid nanofibers. The morphology of the hybrid nanofibers has been characterized in detail. They are featured with tremendously increased specific surface areas and appropriate pore size for adsorption of phosphopeptides with high efficiency. The BC@mTiO₂ tips allow improving both the sensitivity and selectivity of mass spectrometry by nearly two orders of magnitude compared with the commercial tips. As a robust and highly cost-effective platform, our approach has provided a nanotechnology invention to enrich and detect phosphorylated proteins with important biomedical applications.     

EJMS protocol: systematic studies on TiO2-based phosphopeptide enrichment procedures upon in-solution and in-gel digestions of proteins. Are there readily applicable protocols suitable for matrix-assisted laser desorption/ionization mass spectrometry-based phosphopeptide stability estimations?

There have been many successful efforts to enrich phosphopeptides in complex protein mixtures by the use of immobilized metal affinity chromatography (IMAC) and/or metal oxide affinity chromatography (MOAC) with which mass spectrometric analysis of phosphopeptides has become state of the art in specialized laboratories, mostly applying nanoLC electrospray ionization mass spectrometry-based investigations. However, widespread use of these powerful techniques is still not achieved. In this study, we present a ready-to-use phosphopeptide enrichment procedure using commercially available TiO(2)-loaded pipette tips in combination with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analyses. Using α-casein as a model protein and citric acid as additive during sample loading, a similar enrichment success can be achieved as compared to applying 2,5- dihydroxy benzoic acid (DHB) for this task. But the DHB-inherited drawbacks are eliminated. In addition, we show that combining DHB and 2,4,6-trihydroxy acetophenone (THAP) as matrix for MALDI-MS measurements retains the sensitivity of DHB for phosphopeptide analysis but adds the homogenous crystallization properties of THAP, enabling preparation of evenly distributed matrix surfaces on MALDI-MS anchor targets, a prerequisite for automated MALDI- MS analyses. Tripartite motif-containing protein 28 and stathmin are two examples for which successful phosphopeptide enrichment of either sodium dodecyl sulfate polyacrylamide gel electrophoresis or two-dimensional gel electrophoresis-separated proteins is shown. Finally, high resolution MALDI Fourier transform ion cyclotron resonance mass spectrometry after phosphopeptide enrichment suggests that chemical dephosphorylation may occur as a side reaction during basic elution of phosphopeptides bound to MOAC surfaces, suggesting that proteome-wide phosphopeptide analyses ought to be interpreted with caution. In contrast, in-depth analysis of phosphopeptide/non-phosphorylated peptide siblings may be used to estimate stability differences of phosphorylation sites in individual proteins, possibly adding valuable information on biological regulation processes.     

磷酸化蛋白质分析技术在蛋白质组研究中的应用

磷酸化修饰蛋白质的分析是蛋白质组研究中的重要内容。对于目前磷酸化蛋白质分析所涉及的各种方法,包括放射性同位素标记,抗体免疫印记等传统方法和以串联质谱各种扫描技术为基础,结合亲和提取、液相色谱-质谱联用等手段的新技术、新方法,以及这些技术在磷酸化蛋白质组学中的应用予以评述。     

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.