基于功能磁性材料的蛋白质组学分离鉴定新方法研究
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摘要
本论文针对目前蛋白质组学研究中面临的分离富集及鉴定方面的热点难点问题，将功能磁性材料与蛋白质分析结合起来，开展了一系列研究工作，发展了相关的新技术新方法并进行了实际的应用研究，取得了一些创新性研究结果。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目前分离鉴定研究的主要技术手段及分离富集新技术研究的发展趋势；概述了磁性聚合物微球的特点及其应用；就功能材料应用于分离富集低丰度蛋白和翻译后修饰蛋白质的研究进展进行了综述；提出了本论文选题的目的和意义。
第二章针对低丰度蛋白及肽段的分离鉴定，采用水热法制备了具有超顺磁性的四氧化三铁磁性微球；采用溶胶-凝胶法在其表面包覆二氧化硅层，合成制备了具有核壳结构的Fe_3O_4@SiO_2磁性硅球；并在其表面进行硅烷化修饰。利用振动样品磁场计、傅立叶变换红外光谱仪、透射及扫描电子显微镜、热失重分析仪等对我们制备的C8键合相疏水性硅球磁性材料C8-f-Fe_3O_4@SiO_2进行了表征。该材料的硅层表面与报道过的同类材料的聚合物表面相比，具有更好的生物相容性。将其应用于富集低丰度肽段，富集倍数达到100倍以上；即使对高浓度的盐溶液中的肽段仍能实现有效富集。进一步用于血清中游离低丰度肽段的分离富集。实验结果表明，其对于血清中游离肽段的富集效果达到并超过了已经报道的同类材料的效果。
第三章针对翻译后修饰蛋白质组中的磷酸化蛋白及肽段的分离富集问题，采用固定金属亲和色谱(IMAC)原理，在Fe_3O_4@SiO_2磁性硅球表面键合上螯合金属离子的官能团，将Fe(Ⅲ)固定在磁球表面。采用傅立叶变换红外光谱仪等对其进行了表征与确认。
以β-casein标准蛋白为测试对象，实验证明该材料对于磷酸化肽段具有很好的选择性富集效果，信躁比可提高10倍以上。实验得到了该材料选择性富集磷酸化肽段的最佳条件并考察了该材料对于混合蛋白酶解肽段体系中磷酸化肽段的选择性富集性能，富集到的磷酸化肽可洗脱分析也可无需洗脱直接进行质谱分析，显示了该方法的灵活性。在此基础上，进一步用于人血清中游离的磷酸化肽段的富集，并采用质谱进行了磷酸化肽段结构以及磷酸化位点的鉴定，获得了一批磷酸化肽段数据。以鼠肝蛋白提取物为研究对象，将提取蛋白酶解得到的鼠肝肽段混合物，分别采取两条技术路线进行分离鉴定：(a)将肽段混合物中所有的磷酸化肽段富集到材料上，将其洗脱，进行nanoLC-LTQ MS／MS分析，鉴定了66条磷酸化肽段。(b)将肽段混合物进行色谱分离，按时间收集29个馏分，降低了富集体系的复杂性后再用材料富集各个馏分中的磷酸化肽，对每个馏分中富集到的磷酸化肽段采用MALDI TOF MS进行磷酸化肽段及其位点的鉴定，显示了该材料对磷酸化肽段具有较好的选择性和适用性。
论文还发展了更为简便的方法，合成了氨基四氧化三铁磁性纳米材料，在其表面键合上螯合金属离子的官能团，将Fe(Ⅲ)、Al(Ⅲ)、Ga(Ⅲ)、In(Ⅲ)、Zr(Ⅳ)、Ce(Ⅲ)等离子固定到磁球表面。通过傅立叶变换红外光谱仪、能量弥散X射线分析仪等对其进行表征。考察了表面固定Fe(Ⅲ)、Al(Ⅲ)、Ga(Ⅲ)、In(Ⅲ)、Zr(Ⅳ)、Ce(Ⅲ)等离子的氨基四氧化三铁磁性纳米材料对于磷酸化肽段的选择性富集能力，结果表明，所有材料对于磷酸化肽段都有较好的分离富集选择性，其中Fe(Ⅲ)、Al(Ⅲ)、Ga(Ⅲ)和Zr(Ⅳ)较In(Ⅲ)、Ce(Ⅲ)的选择性更加突出。
第四章研究探索了二氧化钛的包覆新方法，采用磁球外部包覆碳层为模板包覆二氧化钛、随后灼烧去除碳层的方法，制备了结构紧密的具有核壳结构的Fe_3O_4@TiO_2超顺磁性微球。该新材料具有与IMAC材料完全不同的富集机理，且具有更高的化学惰性和稳定性。采用振动样品磁场计、傅立叶变换红外光谱仪、透射及扫描电子显微镜等对产物进行了表征与确认。该合成新方法为在磁球表面包覆其他金属氧化物提供了很好的借鉴作用。实验进而优化了该材料富集磷酸化肽段的实验条件，包括富集体系、富集时间、样品洗脱时间等，验证了该材料对于复杂体系中磷酸化肽段有很好的选择性富集性能。并将其应用于人血清磷酸化肽富集和鼠肝蛋白中磷酸化肽鉴定，获得了79条磷酸化肽段的数据。
第五章针对翻译后修饰蛋白中糖基化蛋白及肽段的分离富集问题，论文研究制备了表面键合硼酸基团／Con A凝集素的氨基磁性纳米粒子新材料，采用傅立叶变换红外光谱仪进行表征；对该材料应用于糖基化蛋白的选择性富集进行了初步实验探索，实现了对糖蛋白的选择性富集，获得了有价值的研究结果。论文还研究了糖蛋白的酶解方法，优化了酶解的条件，采用色谱分离的方法获得了目标糖肽段。
总之，本论文围绕蛋白质组学研究的新技术新方法，发展了多种功能化磁性材料并建立了多种有效的分离富集方法，为解决蛋白质组学分析中的低丰度蛋白质、翻译后修饰的磷酸化和糖基化蛋白的分离富集及鉴定问题提供了新颖有效的研究手段和方法。
Based on the proteome research background and the development trend of polymer magnetic microspheres, the research interest of this work focused on preparing several kinds of novel functionalized magnetic polymer microspheres and developing a series of techniques and methods to resolve current problems in the separation and concentration of low-abundance and post-translational proteins. This dissertation is divided into five parts.
In chapter 1, advances in current protein separation and concentration techniques, applications of functionalized magnetic polymer microspheres techniques and application of functional materials in proteome research were summarized in details. The intention and meaning of this dissertation were explained.
In chapter 2, magnetite particles were synthesized via solvothermal reaction; and then magnetite microspheres were coated with silica through sol-gel methd; subsequent modified with chloro(dimethyl) octylsilane;thus a novel C8-functionalized magnetic polymer microsphere was prepared. With the characterization of vibrating-sample magnetometer, FT-IR, TEM, SEM and Thermogravimetric analysis, the resulting C8 functionalized magnetic silica microspheres exhibited well-defined magnetite-core-silica-shell structure and possess high content of magnetite, which endow them with high dispersiblity and excellent magnetic responsibility. As a result of their excellent magnetic property, the synthesized C8 -functionalized magnetic silica microspheres were successfully applied for convenient, fast and efficient enrichment of low-abundance peptides from tryptic protein digest and human serum via a direct MALDI-TOF mass spectrometry analysis. The signal intensity could be improved by at least two orders of magnitude.Even in high salt concentration solution, the peptides could also be isolated effectively. The experiment results were almost the same with the results gained using the C8 -functionalized magnetic silica from Bruker Company in the reference. The facile synthesis and the convenient and efficient enrichment process of the novel C8-functionalize microspheres make it promising candidate for isolation of peptides even in complex biological samples.
Chapter 3 presents a facile way to modify the surface of magnetic silica microspheres and then immobilize Fe~(3+) ions on their surface based on the principle of IMAC, thus Fe~(3+)-immobilized magnetic silica micorspheres (Fe~(3+)-MS) were prepared. We confirmed them with FT-IR, TEM and SEM. Because of high magnetic responsivity to magnetic field and the introduction of Fe~(3+) on the smooth silica coatings, the prepared Fe~(3+)-MS could be applied to efficiently and conveniently enrich trace peptides with a help of applied magnetic field. The Fe~(3+)-MS showed good selectivity to phosphopeptides and the S/N signal could be improved by at least one order of magnitude. The experimental conditions for the enrichement of phosphopeptides were optimized. In more complex sample, phosphopeptides could also be selectively enriched. The captured phosphopeptides could also be direct analysis by MALDI-TOF MS avoiding the sample loss during elution from the material.
The Fe~(3+)-MS were applied to capture the phosphopeptides in complex biological samples. Some phosphopeptides in normal human serum were enriched and their composition and phosphotylated site were determined by MALDI-TOF MS/MS. It was also applied to isolate the phosphopeptieds in trypsin digest of rat liver protein lysate.we took two technical routes: (1) isolated the phosphopeptieds in trypsin digest of rat liver protein lysate, then analyzed the eluted sample by nanoLC- LTQ MS/MS and 66 phosphopeptides were successfully identified. (2) separated the trypsin digest of rat liver protein lysate by RPLC and 29 fractions are collected. Thus the complexity of the fraction was lowered. Then isolated the phosphopeptieds from each fraction and then analyzed the elution by MALDI TOF MS.
In addition to above work, we developed a more convenient method to synthesize a novel functional magnetic material for phosphopeptides isolation. Amine-magnetite nanoparticles were synthesized by solvothermal reaction and were further converted into carboxy-magnetite nanoparticles through two-step amidation reaction. Then, Fe(III)、Al(III)、Ga(III)、In(III)、Zr(IV)、Ce(III) ions were immobilized on the surface of the nanoparticles via chelation respectively which were confirmed by characterization with FT-IR, TEM, SEM and EDXA analysis. All of The six materials showed good selectivities to phosphopeptides, especially Fe(III)、Al(III)、Ga(III) and Zr(IV).
In chapter 4, we present an innovative approach for the synthesis of TiO_2-coated magnetite microspheres (Fe_3O_4@TiO_2 microspheres) with well-defined core-shell structure, which were confirmed by characterization with FT-IR, TEM, SEM and EDXA analysis. This material enriched phosphopeptides by the affinity between TiO_2 and phosphopeptides and was more stable than the IMAC materials. By using the Fe_3O_4@TiO_2 microspheres with the assistance of applied magnetic field, we demonstrate the high efficiency of the smart application of these microspheres as specific capture of phosphopeptides for MALDI-TOF MS analysis. The experimental conditions for the enrichement of phosphopeptides were optimized. In more complex sample, phosphopeptides could also be selectively enriched effectively.The process of enrichment is very facile, efficient and highly selective. The peptides adsorbed on the Fe_3O_4@TiO_2 core-shell microspheres can be directly analyzed by MALDI-TOF-MS analysis without elution from the Fe_3O_4@TiO_2 core/shell microspheres.
The Fe_3O_4@TiO_2 core-shell microspheres were applied to capture the phosphopeptides in normal human serum. Two phosphopeptides were enriched and their composition and phosphotylated site were determined by MALDI-TOF MS/MS. It was also applied to isolate the phosphopeptieds in trypsin digest of rat liver protein lysate and then the eluted sample was analyze by nanoLC- LTQ MS/MS and 79 phosphopeptides were successfully identified. These results are expected to open up a new possibility for the enrichment of phosphopeptides. Moreover, the versatile, low-cost and reproducible synthesis method could extend to other core-shell structured microspheres of metal oxides.
In chapter 5, the boronic acid or Con A modified magnetic nanopartiles were synthesize and applied to selectively enrich glycoprotein from protein mixture.the experimnt result indicated that the boronic acid modified magnetic nanopartiles effectively captured the glycoprotein. In addition, the digest conditions of glycoprotein were modified and glycopeptides were separated from the digest mixture by RPLC and then confirmed by MALDI-TOF-MS.
In summary, the main contributes of this dissertation is to develop several functional magnetic materials and found several new separation methods for low-abundance and post-translational proteins. We aim at exploring and finding out new techniques in the separtion and concentration of proteome research fields, so that more breakthroughs can be obtained in the proteome research study.
第一章概述了蛋白质组学目前分离鉴定研究的主要技术手段及分离富集新技术研究的发展趋势；概述了磁性聚合物微球的特点及其应用；就功能材料应用于分离富集低丰度蛋白和翻译后修饰蛋白质的研究进展进行了综述；提出了本论文选题的目的和意义。
第二章针对低丰度蛋白及肽段的分离鉴定，采用水热法制备了具有超顺磁性的四氧化三铁磁性微球；采用溶胶-凝胶法在其表面包覆二氧化硅层，合成制备了具有核壳结构的Fe_3O_4@SiO_2磁性硅球；并在其表面进行硅烷化修饰。利用振动样品磁场计、傅立叶变换红外光谱仪、透射及扫描电子显微镜、热失重分析仪等对我们制备的C8键合相疏水性硅球磁性材料C8-f-Fe_3O_4@SiO_2进行了表征。该材料的硅层表面与报道过的同类材料的聚合物表面相比，具有更好的生物相容性。将其应用于富集低丰度肽段，富集倍数达到100倍以上；即使对高浓度的盐溶液中的肽段仍能实现有效富集。进一步用于血清中游离低丰度肽段的分离富集。实验结果表明，其对于血清中游离肽段的富集效果达到并超过了已经报道的同类材料的效果。
第三章针对翻译后修饰蛋白质组中的磷酸化蛋白及肽段的分离富集问题，采用固定金属亲和色谱(IMAC)原理，在Fe_3O_4@SiO_2磁性硅球表面键合上螯合金属离子的官能团，将Fe(Ⅲ)固定在磁球表面。采用傅立叶变换红外光谱仪等对其进行了表征与确认。
以β-casein标准蛋白为测试对象，实验证明该材料对于磷酸化肽段具有很好的选择性富集效果，信躁比可提高10倍以上。实验得到了该材料选择性富集磷酸化肽段的最佳条件并考察了该材料对于混合蛋白酶解肽段体系中磷酸化肽段的选择性富集性能，富集到的磷酸化肽可洗脱分析也可无需洗脱直接进行质谱分析，显示了该方法的灵活性。在此基础上，进一步用于人血清中游离的磷酸化肽段的富集，并采用质谱进行了磷酸化肽段结构以及磷酸化位点的鉴定，获得了一批磷酸化肽段数据。以鼠肝蛋白提取物为研究对象，将提取蛋白酶解得到的鼠肝肽段混合物，分别采取两条技术路线进行分离鉴定：(a)将肽段混合物中所有的磷酸化肽段富集到材料上，将其洗脱，进行nanoLC-LTQ MS／MS分析，鉴定了66条磷酸化肽段。(b)将肽段混合物进行色谱分离，按时间收集29个馏分，降低了富集体系的复杂性后再用材料富集各个馏分中的磷酸化肽，对每个馏分中富集到的磷酸化肽段采用MALDI TOF MS进行磷酸化肽段及其位点的鉴定，显示了该材料对磷酸化肽段具有较好的选择性和适用性。
论文还发展了更为简便的方法，合成了氨基四氧化三铁磁性纳米材料，在其表面键合上螯合金属离子的官能团，将Fe(Ⅲ)、Al(Ⅲ)、Ga(Ⅲ)、In(Ⅲ)、Zr(Ⅳ)、Ce(Ⅲ)等离子固定到磁球表面。通过傅立叶变换红外光谱仪、能量弥散X射线分析仪等对其进行表征。考察了表面固定Fe(Ⅲ)、Al(Ⅲ)、Ga(Ⅲ)、In(Ⅲ)、Zr(Ⅳ)、Ce(Ⅲ)等离子的氨基四氧化三铁磁性纳米材料对于磷酸化肽段的选择性富集能力，结果表明，所有材料对于磷酸化肽段都有较好的分离富集选择性，其中Fe(Ⅲ)、Al(Ⅲ)、Ga(Ⅲ)和Zr(Ⅳ)较In(Ⅲ)、Ce(Ⅲ)的选择性更加突出。
第四章研究探索了二氧化钛的包覆新方法，采用磁球外部包覆碳层为模板包覆二氧化钛、随后灼烧去除碳层的方法，制备了结构紧密的具有核壳结构的Fe_3O_4@TiO_2超顺磁性微球。该新材料具有与IMAC材料完全不同的富集机理，且具有更高的化学惰性和稳定性。采用振动样品磁场计、傅立叶变换红外光谱仪、透射及扫描电子显微镜等对产物进行了表征与确认。该合成新方法为在磁球表面包覆其他金属氧化物提供了很好的借鉴作用。实验进而优化了该材料富集磷酸化肽段的实验条件，包括富集体系、富集时间、样品洗脱时间等，验证了该材料对于复杂体系中磷酸化肽段有很好的选择性富集性能。并将其应用于人血清磷酸化肽富集和鼠肝蛋白中磷酸化肽鉴定，获得了79条磷酸化肽段的数据。
第五章针对翻译后修饰蛋白中糖基化蛋白及肽段的分离富集问题，论文研究制备了表面键合硼酸基团／Con A凝集素的氨基磁性纳米粒子新材料，采用傅立叶变换红外光谱仪进行表征；对该材料应用于糖基化蛋白的选择性富集进行了初步实验探索，实现了对糖蛋白的选择性富集，获得了有价值的研究结果。论文还研究了糖蛋白的酶解方法，优化了酶解的条件，采用色谱分离的方法获得了目标糖肽段。
总之，本论文围绕蛋白质组学研究的新技术新方法，发展了多种功能化磁性材料并建立了多种有效的分离富集方法，为解决蛋白质组学分析中的低丰度蛋白质、翻译后修饰的磷酸化和糖基化蛋白的分离富集及鉴定问题提供了新颖有效的研究手段和方法。
Based on the proteome research background and the development trend of polymer magnetic microspheres, the research interest of this work focused on preparing several kinds of novel functionalized magnetic polymer microspheres and developing a series of techniques and methods to resolve current problems in the separation and concentration of low-abundance and post-translational proteins. This dissertation is divided into five parts.
In chapter 1, advances in current protein separation and concentration techniques, applications of functionalized magnetic polymer microspheres techniques and application of functional materials in proteome research were summarized in details. The intention and meaning of this dissertation were explained.
In chapter 2, magnetite particles were synthesized via solvothermal reaction; and then magnetite microspheres were coated with silica through sol-gel methd; subsequent modified with chloro(dimethyl) octylsilane;thus a novel C8-functionalized magnetic polymer microsphere was prepared. With the characterization of vibrating-sample magnetometer, FT-IR, TEM, SEM and Thermogravimetric analysis, the resulting C8 functionalized magnetic silica microspheres exhibited well-defined magnetite-core-silica-shell structure and possess high content of magnetite, which endow them with high dispersiblity and excellent magnetic responsibility. As a result of their excellent magnetic property, the synthesized C8 -functionalized magnetic silica microspheres were successfully applied for convenient, fast and efficient enrichment of low-abundance peptides from tryptic protein digest and human serum via a direct MALDI-TOF mass spectrometry analysis. The signal intensity could be improved by at least two orders of magnitude.Even in high salt concentration solution, the peptides could also be isolated effectively. The experiment results were almost the same with the results gained using the C8 -functionalized magnetic silica from Bruker Company in the reference. The facile synthesis and the convenient and efficient enrichment process of the novel C8-functionalize microspheres make it promising candidate for isolation of peptides even in complex biological samples.
Chapter 3 presents a facile way to modify the surface of magnetic silica microspheres and then immobilize Fe~(3+) ions on their surface based on the principle of IMAC, thus Fe~(3+)-immobilized magnetic silica micorspheres (Fe~(3+)-MS) were prepared. We confirmed them with FT-IR, TEM and SEM. Because of high magnetic responsivity to magnetic field and the introduction of Fe~(3+) on the smooth silica coatings, the prepared Fe~(3+)-MS could be applied to efficiently and conveniently enrich trace peptides with a help of applied magnetic field. The Fe~(3+)-MS showed good selectivity to phosphopeptides and the S/N signal could be improved by at least one order of magnitude. The experimental conditions for the enrichement of phosphopeptides were optimized. In more complex sample, phosphopeptides could also be selectively enriched. The captured phosphopeptides could also be direct analysis by MALDI-TOF MS avoiding the sample loss during elution from the material.
The Fe~(3+)-MS were applied to capture the phosphopeptides in complex biological samples. Some phosphopeptides in normal human serum were enriched and their composition and phosphotylated site were determined by MALDI-TOF MS/MS. It was also applied to isolate the phosphopeptieds in trypsin digest of rat liver protein lysate.we took two technical routes: (1) isolated the phosphopeptieds in trypsin digest of rat liver protein lysate, then analyzed the eluted sample by nanoLC- LTQ MS/MS and 66 phosphopeptides were successfully identified. (2) separated the trypsin digest of rat liver protein lysate by RPLC and 29 fractions are collected. Thus the complexity of the fraction was lowered. Then isolated the phosphopeptieds from each fraction and then analyzed the elution by MALDI TOF MS.
In addition to above work, we developed a more convenient method to synthesize a novel functional magnetic material for phosphopeptides isolation. Amine-magnetite nanoparticles were synthesized by solvothermal reaction and were further converted into carboxy-magnetite nanoparticles through two-step amidation reaction. Then, Fe(III)、Al(III)、Ga(III)、In(III)、Zr(IV)、Ce(III) ions were immobilized on the surface of the nanoparticles via chelation respectively which were confirmed by characterization with FT-IR, TEM, SEM and EDXA analysis. All of The six materials showed good selectivities to phosphopeptides, especially Fe(III)、Al(III)、Ga(III) and Zr(IV).
In chapter 4, we present an innovative approach for the synthesis of TiO_2-coated magnetite microspheres (Fe_3O_4@TiO_2 microspheres) with well-defined core-shell structure, which were confirmed by characterization with FT-IR, TEM, SEM and EDXA analysis. This material enriched phosphopeptides by the affinity between TiO_2 and phosphopeptides and was more stable than the IMAC materials. By using the Fe_3O_4@TiO_2 microspheres with the assistance of applied magnetic field, we demonstrate the high efficiency of the smart application of these microspheres as specific capture of phosphopeptides for MALDI-TOF MS analysis. The experimental conditions for the enrichement of phosphopeptides were optimized. In more complex sample, phosphopeptides could also be selectively enriched effectively.The process of enrichment is very facile, efficient and highly selective. The peptides adsorbed on the Fe_3O_4@TiO_2 core-shell microspheres can be directly analyzed by MALDI-TOF-MS analysis without elution from the Fe_3O_4@TiO_2 core/shell microspheres.
The Fe_3O_4@TiO_2 core-shell microspheres were applied to capture the phosphopeptides in normal human serum. Two phosphopeptides were enriched and their composition and phosphotylated site were determined by MALDI-TOF MS/MS. It was also applied to isolate the phosphopeptieds in trypsin digest of rat liver protein lysate and then the eluted sample was analyze by nanoLC- LTQ MS/MS and 79 phosphopeptides were successfully identified. These results are expected to open up a new possibility for the enrichment of phosphopeptides. Moreover, the versatile, low-cost and reproducible synthesis method could extend to other core-shell structured microspheres of metal oxides.
In chapter 5, the boronic acid or Con A modified magnetic nanopartiles were synthesize and applied to selectively enrich glycoprotein from protein mixture.the experimnt result indicated that the boronic acid modified magnetic nanopartiles effectively captured the glycoprotein. In addition, the digest conditions of glycoprotein were modified and glycopeptides were separated from the digest mixture by RPLC and then confirmed by MALDI-TOF-MS.
In summary, the main contributes of this dissertation is to develop several functional magnetic materials and found several new separation methods for low-abundance and post-translational proteins. We aim at exploring and finding out new techniques in the separtion and concentration of proteome research fields, so that more breakthroughs can be obtained in the proteome research study.
引文
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