蛋白质组学中高灵敏度高特异性的生物质谱新方法研究

【作者】 许亚伟；

【导师】 陆豪杰；

【作者基本信息】 复旦大学 ， 分析化学， 2011， 博士

【摘要】 本论文针对目前蛋白质组学研究中的热点问题,将纳米无机材料、介孔无机材料、材料表面官能化与多肽化学修饰的方法结合起来,开展了一系列的研究工作。发展了一系列针对小分子化合物、磷酸化修饰蛋白质与糖基化修饰蛋白质的新技术与新方法,并进行了应用型研究,取得了一些创新性成果。本论文主要发展了适用于小分子及糖类的新型MALDI无机基质；针对磷酸化修饰,将化学衍生技术应用于多肽羧基,大幅度提高了磷酸化多肽的离子化效率；还将硼酸基团修饰的无机介孔材料应用与糖基化多肽的富集,并随后发展出了糖基化多肽的靶上富集技术。主要研究内容和取得的主要研究成果摘要如下：第一章概述了蛋白质组学的发展现状,简要介绍了蛋白质组学研究中最重要的几项技术及其在当今生物科学研究中的地位和作用。阐述了激光解吸离子源质谱(Matrix-assisted laser desorption/ionization mass spectrometer, MALDI-MS)在蛋白质组学中应用的现状与主要困难。介绍了MALDI基质在整个离子化过程中的重要作用并概述了MALDI基质的发展历程与面临的主要困难。对蛋白质翻译后修饰中最为重要的两类(磷酸化与糖基化)后修饰的生物学意义以及主要研究方法进行了综述。在此基础上,提出了本论文选题的目的和意义。主要内容和主要成果将在以下几章的摘要中逐一简述。第二章针对常规有机MALDI基质容易产生大量低分子量端噪音的问题,将柠檬酸氢铵参杂的纳米二氧化钛作为MALDI基质,用于分析小分子化合物与糖类。本章介绍了无机MALDI基质的概况与发展该新型基质的意义。详细阐述了该新型无机基质的制备与使用方法。与传统有机基质CHCA相比,该氧化钛基质具有下列几个优点：首先,纳米氧化钛成本极低,远低于常用有机基质的价格。而且基质制备方法简单,无需复杂处理；其次,氧化钛基质本身不电离,只有参杂的柠檬酸氢铵会产生两个碱金属加和峰,很容易辨识。因而大大简化了低分子量端的质谱图,适用于分析小分子；第三,可以分析糖类等通常难以被MALDI质谱检测的化合物；第四,样品分布均匀,重现性好,可以对样品进行定量分析；最后,对小分子具有很高的灵敏度,例如对蔗糖和p环糊精可以达到纳摩尔级的检测限。试验结果表明,柠檬酸氢铵参杂的纳米氧化钛基质成功地实现了对分子量1200以内的小分子的定性与定量分析。第三章针对磷酸化修饰的多肽离子化效率低、容易受到非磷酸化多肽的压制导致难以被质谱检测的问题,发展了使用1-(2-嘧啶基)哌嗪(1-(2-pyrimidyl)piperazine,PP)来修饰多肽羧基,从而实现大幅度提高磷酸化多肽的离子化效率并显著减弱非磷酸化多肽的压制效应的目的。本章概述了蛋白质磷酸化的重要生物学意义,介绍了磷酸化研究的主要方法与现状,并阐述了发展该方法的重要意义。采用1-(2-嘧啶基)哌嗪(1-(2-pyrimidyl)piperazine, PP)修饰多肽羧基可以增加多肽的等电点、气象碱性度和疏水性,从而提高多肽在MALDI源与ESI源中的离子化效率。尽管本方法无差别地修饰所有多肽中含有的所有羧基,但是磷酸化多肽经PP羧基衍生后离子化效率提高的倍数远大于非磷酸化多肽。因此,在混合体系中难以直接检测的磷酸化多肽经过PP羧基衍生后信号强度相比于非磷酸化多肽显著增强,从而实现了不需要经过质谱前磷酸化多肽特异性预富集而使磷酸化多肽得到检测的目的。与传统方法相比,本方法消耗更少的样品量和更少的时间,同时避免了传统化学修饰方法产率低、反应条件苛刻和副反应多的问题。第四章针对糖基化后修饰研究中糖基化多肽含量低、结构复杂、离子化效率较低并且现有富集方法综合性能不高的问题,发展了一种基于硼酸官能化的介孔二氧化硅材料的特异性富集方法,从而显著改善了糖基化多肽质谱预富集方法效率不高、适用性不广的问题。本章概述了糖基化研究的重要性及其面临的主要困难,介绍了现有的特异性富集糖基化修饰的方法,并阐述了发展该新型富集方法的目的与意义。由于硼酸可以与顺式二羟基形成共价键(醚键)从而成为五元环。因而这一反应具有广泛的适用性：无论是来自N-糖或O-糖还是任意糖型的顺式二羟基都可以与硼酸发生化学反应并成键。根据这一原理,我们将硼酸作为表面官能团嫁接于载体表面,使其具有捕获糖基化多肽的能力；同时,我们选择具有高比表面积的介孔二氧化硅作为载体,以期实现对糖基化多肽的高特异性富集。本章介绍了硼酸修饰的介孔二氧化硅的结构特征与合成方法,对其结构进行了严谨的表征。通过对其富集性能的详细分析与考察,我们发现使用该复合介孔材料来富集糖基化多肽具有传统富集方法无可比拟的优点。首先,它的合成过程简单,全部在温和的温度与中性条件下进行。第二,该复合介孔材料具有的高比表面积,这大大促进了其与糖基化多肽的结合速率,使得样品孵育时间缩短到短短的15分钟。第三,该材料表面具备的丰富的硼酸基团大大减少了非特异性吸附。即使在大量胰酶酶解的牛血清白蛋白(BSA)的非糖基化多肽存在的条件下,依然没有发现非糖基化多肽被非特异性吸附下来。因此,去掉了大量非糖基化多肽带来的信号被压制的问题,糖基化多肽的检测灵敏度得到了很大提高。通过富集效应的进一步浓缩,使得糖基化多肽的检测限提高了两个数量级左右。最后,高比表面积和表面大量的硼酸基团也使该复合材料具备很高的回收率,通过同位素标记的办法,测得该方法针对糖基化多肽的回收率达到83.5%。因此,本章阐述的基于硼酸修饰的介孔二氧化硅材料富集法,可以实现对不同种类的糖基化多肽的高特异性快速、高效地富集。第五章针对糖基化多肽的基质辅助激光解吸离子源(MALDI)靶上富集方法尚为空白的现状,发展了一种使用硼酸修饰的镀金硅片进行MALDI靶上富集糖基化多肽的方法,从而填补了没有MALDI靶上富集糖基化多肽方法的空白,走出了使用MALDI-MS分析糖基化多肽预处理繁琐的困境。本章概述了MALDI-MS在蛋白质组学研究中的重要性,介绍了现有的MALDI靶上样品预处理技术的现状,并简要介绍了糖基化修饰质谱预富集方法。由于MALDI靶上富集糖基化多肽的技术仍未见报道,我们发展了使用硼酸修饰的镀金硅片进行MALDI靶板上富集糖基化多肽的新方法。该方法所使用的新型MALDI靶板的制备过程在本章中进行了详细的阐述与表征。采用多种糖基化蛋白的标准酶解产物对该方法进行了考察。从试验结果来看,该靶上富集糖基化多肽的方法具有很多优点：首先,硼酸修饰的镀金硅片的合成方法非常简单,全过程不涉及任何苛刻或者剧烈的反应条件,而且只需要不到24小时。其次,与已报道的靶上富集方法不同,本章所述的方法将官能团嫁接在小尺寸的镀金硅片表面,而非直接嫁接在商品化靶板表面。这给该方法的应用带来极大的灵活性,既可以直接在靶上富集小体积样本,也可以浸入溶液中富集大体积样本。第三,该方法可以减少不必要的样本损失同时去除非糖基化多肽的压制效应,这使得糖基化多肽的检测限提高了约两个数量级。第四,该方法具有很高的回收率,达到65.8%,这几乎是己报道的靶上富集方法的最高水平。最后,在富集糖基化多肽的同时,该方法还可以去除样本中的盐类,例如碳酸氢铵和磷酸盐缓冲液(PBS)中的盐类。因此,采用硼酸修饰的镀金硅片不但可以快速有效地富集糖基化多肽,同时还能有效地一步除盐。第六章针对O-糖基化修饰研究中O-糖位点鉴定困难,糖肽离子化效率较低的问题,发展了一种p消除与迈克尔加成反应辅助的O-糖基化多肽质谱分析的新方法,以期大幅度提高O-糖基化多肽的离子化效率,同时标记O-糖基化位点以辅助O-糖基化位点的鉴定。本章概述了O-糖基化修饰的生物学意义,简要介绍了O-糖基化研究所面临的挑战：缺乏广泛适用的糖苷内切酶；移除糖链的化学方法缺陷明显；糖肽离子化效率低；移除糖链后的糖基化位点难以分析。针对这些问题,我们尝试发展一种依靠化学方法消除O-糖链,随后在同一糖基化位点上通过迈克尔加成反应在该位点上加成一个硫代胆碱分子。由于硫代胆碱分子的分子量为120,可以给O-糖基化位点上加成一个分子量较大的标签,可以辅助O-糖基化位点的鉴定。其次,硫代胆碱上的季铵基团带有正电荷,可以显著促进O-糖基化多肽的离子化,提高其离子化效率。第三,通过酶促反应的方法制备的硫代胆碱省去了复杂化学合成步骤,降低了使用硫代胆碱的门槛,同时还避免了产物中带来的杂质。最后,我们期望通过硫代胆碱的标记可以同时给O-糖基化多肽的定量分析带来一种新的解决方法,以期在未来的大规模应用中显著降低O-糖基化研究的难度。总而言之,本论文围绕蛋白质组学与质谱相关的技术,发展了多种辅助分析小分子、糖类、磷酸化多肽与糖基化多肽的新技术与新方法,为解决蛋白质组学中小分子、磷酸化修饰与糖基化修饰的检测灵敏度低、特异性差的问题提供了新颖有效的研究手段与研究方法。更多还原

【Abstract】 This dissertation is focusing on developing novel methods for proteomics research based on bio-mass spectrometry. The purpose of this research is about how to analyze targeted bio-molecules with a higher sensitivity and higher selectivity. In this dissertation, it demonstrates five newly developed methods which combine some cutting edge tenichques, such as nano material, mesoporous material, surface functionalization and peptide derivatization. In the following part, I will give a brief introduction of the six chapters of this dissertation.In the first chapter, the development of proteomics research was briefly reviewed. Several important methods and tools in this field were introduced. One of the most important soft ionization ion sources, matrix-assisted laser desorption/ionization (MALDI) source was reviewed. The application and major challenges of MALDI-MS was summarized. As the most important part of MALDI process, the MALDI matrix was reviewed in detail including both inorganic matrices and organic matrices. Besides, two of the most important protein post-translational modifications (PTMs), phosphorylation and glycosylation were reviewed. The recent development and several major reseach methods of these two PTMs were discussed in detail. Based on all these backgrounds, the intention and meaning of this dissertation were explained.In the second chapter, a diammoniu citrate doped TiO2 nanoparticles (TiO2DC) was investigated and evaluated as an inorganic MALDI matrix for molecules with masses ranging from 100 to more than 1000 Da. In comparison with traditional organic matrices and other inorganic matrices, the TiO2DC matrix offers several advantages:(a) low cost and simple sample preparation, (b) applicable to several kinds of analytes, (c) high ionization efficiency and low detection limit, (d) quantitative analysis for small molecule (m/z<1200). The limits of detection at a S/N ratio of 3 are down to 5.6 and 9.5 nM for sucrose andβ-CD. However, the sensitivity of DHC is relatively low. When we perform quantitative analysis with glucose, sucrose and P-CD, the linearity of each sample is pretty good (R2>0.98). According to these results, we believe that the TiO2DC matrix could be potentially used for both qualitative and quantitative analysis.In the third chapter, a chemical derivatization method of peptide carboxy groups with 1-(2-pPyrimidyl)piperazine (PP) was introduced to enhance the ionization efficiencies of peptides especially that of phosphopeptides and make them MS detectable without any specific enrichment. Once carboxy groups were derivatized with PP, the hydrophobicities, pI values and gas-phase basicities of phosphopeptides were largely increased so that the ionization efficiencies could be dramatically enhanced accordingly. As PP derivatization neutralizes the extra negative charges and decreases the hydrophilicities brought in by phosphate groups, the ionization efficiencies of phosphopeptides can be increased up to 101-fold. Comparing with other methods, this brand newimproved technique method needs less sample amount, costs less time and lacks any drawback of traditional derivatization methods such as low yields, harsh reaction conditions and unknown side reactions. This new method has been applied to both standard peptides and tryptic protein digests, and was proved to be very efficient and extremely powerful. We also expect it will be very promising in large-scale phosphoproteome and proteome analysis in the near future.In the fourth chapter, a novel di-boronic acid functionalized mesoporous silica (FDU-12-FG) was synthesized to specifically enrich glycopeptides. This developed FDU-12-GA matrix, with high surface area, large pore volume, and well-defined large sizes of pore cavities and entrances, leads to great advantages in glyco-specific enrichment. Firstly, the synthesis of FDU-12-GA is quite simple under moderate temperature and neutral conditions. Secondly, the large specific surface area greatly increases its binding rate, and the entire loading time needs only 15 min. With the plentiful di-boronic acid function groups on the surface, no nonspecific binding is observed in the presence of prominent tryptic BSA, demonstrating specificity of binding. By capturing and concentrating target glycopeptides, the suppression effect from nonglycopeptides can be eliminated, the LOD of glycopeptides is enhanced by close to two orders of magnitude, and the recovery of the enriched glycopeptides is up to 83.5%. Accordingly, with our newly developed method, various kinds of N-glycopeptides could be specifically selected and enriched for further analysis. We also expect it could be further applied to complex biology samples and glycoproteomics.In the fifth chapter, a method usingdi-boronic acid modified gold-coated Si wafer as MALDI target to enrich glycopeptides was introduced. This on-plate enrichment method has several advantages. Firstly, the synthesis procedure is simple and efficient in which no harsh conditions were needed and the whole process was less than 24 hr. Secondly, unlike previously published on-plate enrichment methods, which employed the strategy of direct modifying commercial MALDI plates, small pieces of SiAuB was used instead of commercial MALDI plate in our method. This characteristic makes it suitable for different samples and various purposes. Thirdly, minimizing the sample loss and eliminating the suppression effect have increased the detection limits of glycopeptides by two orders of magnitude. Furthermore, this is a recoverable method and the recovery of glycopeptides is up to 65.8%. At the same time, high concentration of ABC and physiological buffer PBS can also be removed through on-plate enrichment and no additional desalting step was needed. With this method, glycopeptides can be selectively and effectively enriched. It is a potentially powerful tool for high throughput glycoproteome research.In the sixth chapter, a method focusing on O-glycosylated peptide research was introduced and evaluated. Combining the process ofβelimination and Micheal addition, the O-linked glycan could be eliminated and a nucleophilic molecule could be added onto the O-glycosylation site. Thiocholine was adopted as the addition molecule in order to label the O-glycosylation site and improve the ionization efficiency of O-glycopeptide at the same time. Comparing with the former methods, this method gives several advantages. Firstly, the molecule weight of thiocholine is 120, which is large enough to label the O-glycosylation site. This would make the identification of O-glycosylation site much easier. Secondly, thiocholine carries a positive charge which could facilitate the ionization process of glycopeptide at the positive mode. This would dramatically enhance the ionization efficiency of O-linked glycopeptide. Thirdly, thiocholine was prepared through an enzymatic process which is easy to handle and the product is relatively pure. Finally, this method might be able to be applied to quanlitative analysis of O-glycosylation in future.In summary, this dissertation is focusing on proteomics and bio-mass spectrometry related methodology research. Five novel methods about high sensitivity and high selectivity detection of biological samples were demonstrated. We are trying to develop new methods in the analysis of biological samples, so that more breakthroughs can be obtained in the proteome research in the future.更多还原