生物质谱新技术与新方法及其在蛋白质组学中的应用研究
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摘要
本博士学位论文工作的主要贡献为：在蛋白质组学领域中关于低丰度蛋白和多肽除盐、富集的研究方面取得了创新性的进展：利用液滴内部的“Outward
Flow”过程结合自制的多功能疏水性聚合物成功实现了一步高效靶上除盐与样品富集直接MALDI-MS分析，并成功应用到实际样品的蛋白质组学研究中；同时利用上述体系，使用阳离子型聚合物成功实现了对低丰度磷酸化肽段的靶上富集与除盐；首次利用聚合物-无机纳米复合材料成功实现了低丰度蛋白质／多肽的高效、快速和高回收率富集；参与研制成功了作为高效液相色谱检测器的电喷雾—四极杆—飞行时间质谱仪(ESI-Q-TOF-MS)，填补了国内空白。
蛋白质组学作为后基因组时代生命科学领域的热点，近年来得到了蓬勃的发展，已涉足生命科学中一系列前沿领域，并成为分析化学研究领域的最前沿课题。它的内容包括分离和分析细胞与组织的全部蛋白并直接找到一组或几组功能蛋白，研究它们与功能基因(组)的内在联系。蛋白质组研究具有观察由多基因事件引起的多蛋白质组分整体变化的独特优势，更接近生命现象的本质，在药靶研究中具有潜在价值，可通过对蛋白质性质、丰度的考察来揭示它的功能，进而找到与人类重大疾病相关的差异蛋白，使之成为诊断、治疗及药物筛选的靶分子。目前蛋白质组已被广泛用于研究各种疾病的发生、发展规律，并取得了很多重大的成就。
蛋白质组学的科学研究之所以能够取得蓬勃的发展，主要依赖于生物质谱技术的飞速发展以及高通量分离和分析技术的突破性进步。首先是质谱技术尤其是“软电离源”技术——电喷雾和基质辅助激光解析离子源的发展，使之成为检测微量甚至是痕量蛋白质分子的重要手段。高通量、高效的分离技术和大规模、高效率、高准确性地鉴定一个组织或细胞乃至亚细胞中的全部蛋白质以及利用稳定同位素标记方式与多维分离-串级质谱实现大规模的蛋白质定量分析也已经使得生物质谱成为实现这一目标的核心分析技术。生物信息学的建立形成了国际性的科学大协作。目前，世界各主要国家都不惜巨资进行蛋白质组的研究。蛋白质组学研究的进一步深入，将对了解疾病的发生和药物的筛选起到决定性的作用。
本博士学位论文工作主要是在化学系生物质谱实验室和生物医学研究院蛋白质组学研究中心完成的。由于传统的生物质谱技术平台已不足以应对蛋白质组学中低丰度蛋白检测的要求，所以研究和发展针对低丰度蛋白检测方面的新技术
与新方法尤显得意义重大，本论文以此为切入点，研究了蛋白质组学分析中如何实现低丰度蛋白有效富集和除盐的问题，包括：利用疏水性聚合物微印迹技术实现的靶上一步除盐和样品富集技术；开展了靶上磷酸化肽段直接浓缩与除盐技术的研究；发展了利用聚合物-无机纳米复合材料实现的低丰度蛋白快速高效富集技术。又因为串级质谱的成功鉴定对于蛋白质组学研究也非常重要，所以本论文以一种含有多达28个氨基酸的复杂多肽为对象研究了如何对大质量多肽进行有效的串级质谱全序列分析；本论文作者还参与研制成功了作为高效液相色谱检测器的高分辩飞行时间质谱仪。
本论文共分六章，主要内容摘要如下：
第一章主要综述了蛋白质组学研究中的关键技术——生物质谱相关技术的发展及其在蛋白质组学中的应用。新的“软电离”方式——基质辅助激光解吸电离技术(MALDI)和电喷雾电离技术(ESI)的问世、质谱质量分析器的改善、各种分离技术如高效液相色谱／毛细管电泳等和质谱的联用、稳定同位素标记技术的发展及应用，使得生物质谱已成为蛋白质组学研究中无可替代的核心技术平台。生物质谱在对基因工程产物、功能蛋白及疾病相关蛋白的定性、定量分析中具有无可比拟的优越性，在蛋白的相互作用、蛋白质的折叠等动力学过程的研究中具有极大的潜力。而蛋白质组学作为一门新兴学科，它的发展现状和最新技术进展还包括双向凝胶电泳技术、色谱分离技术、蛋白质芯片技术、酵母双杂交技术和串联亲和纯化技术等。低丰度蛋白的分析与鉴定是蛋白质组学研究的重点和难点内容之一，在生物体中承担重要生命活动的蛋白往往都是低丰度蛋白，然而其极低的含量给后续的分析和检测带来困难，限制了人们对它们的研究和认识，因此低丰度蛋白的有效浓缩与除盐是实现其准确分析和鉴定的重要条件，所以本章还综述了目前针对低丰度蛋白检测的技术，并提出了本课题工作的研究方向。
第二章研究工作主要涉及关于低丰度蛋白靶上一步除盐与富集直接MALDI-MS分析的新方法。这部分工作是通过将疏水性聚合物微印迹技术与基质辅助激光解析离子化质谱联用，巧妙利用液滴内部的“Outward Flow”效应，结合自制的多功能疏水性聚合物成功实现了痕量多肽的靶上一步除盐与富集。微印迹的疏水性聚合物对蛋白质和多肽有很好的吸附富集效果，但是对无机盐和其他污染物吸附很少，利用固体表面液珠蒸发过程中的外流作用，被疏水性聚合物吸附的样品无需额外的洗脱除盐步骤就可实现一步除盐并可直接进行MALDI-TOF-MS分析。本方法不仅成功实现了样品一步除盐与富集的特性，而且具有灵敏度高、重现性高、通量高、耐盐能力强、经济和省时等特点。可广泛用于蛋白质组学领域，大大拓展了疏水性聚合物的应用范围。此工作已显现出比传
统商业Ziptip或ZipPlate除盐、富集系统更优秀的特性，并成功应用在我们课题组承担的国际人类蛋白质组人肝计划和中国人肝计划。
第三章主要阐述了低丰度磷酸化肽段靶上浓缩与除盐—直接MALDI-MS分析的研究。蛋白质的翻译后修饰是目前蛋白质组研究中的一个重要课题，目前蛋白质组技术研究的主要目标之一是建立一套能快速、有效、高通量地分析鉴定发生翻译后修饰的蛋白质的方法技术。而蛋白质磷酸化是最常见、最重要的一种蛋白翻译后修饰方式。蛋白质磷酸化和去磷酸化几乎调节着生命活动的整个过程，包括细胞的增殖、发育和分化、神经活动、肌肉收缩、新陈代谢、肿瘤发生等。目前蛋白质组学方法中磷酸化蛋白、肽段的富集技术主要包括双向磷酸多肽谱图法、高分辨率的凝胶电泳法(2DE)、反相高效液相色谱法、固定化金属亲和色谱(IMAC)、抗体富集、化学标记富集等。磷酸化肽段的质谱检测难点主要在于其丰度低、动态的体内磷酸化过程、难于离子化、受其它高丰度的非磷酸化肽段信号的强烈抑制等原因。本论文采用一种阳离子性聚合物材料，结合第二章介绍的一步除盐与样品富集体系，在靶上有效富集了低浓度磷酸化肽段，大大简化了样品富集步骤。本方法可检测到10fmol／μL β-酪蛋白中的单磷酸化肽，并可得到很好的串级质谱信息。
第四章研究工作主要涉及一种以纳米碳酸钙球表面原位聚合聚甲基丙烯酸甲酯组合材料(简称CaCO_3-PMMA)作为纳米吸附剂，进行痕量肽及蛋白样品的富集——伴随无固态颗粒化基质辅助激光解析离子源质谱直接分析的方法。此聚合物-无机纳米复合材料可对蛋白质和多肽进行快速高效富集，与基质辅助激光解吸离子源质谱有很好的相容性，吸附了样品的CaCO_3-PMMA在进入质谱分析前被巧妙的去核——从而避免固体颗粒对信号重现性的影响及其溅射对质谱仪器的损害。本方法操作简单，快速高效，既避免了常规吹干富集方法的样品损失问题，又具有很好的耐盐性。本方法可广泛适用于蛋白质组学相关领域，并大大拓展了聚合物-无机纳米复合材料CaCO_3-PMMA的应用范围。
第五章主要介绍了对含有28个氨基酸的复杂多肽的串级质谱全序列分析研究。对于含有太多氨基酸片断(大于20个)的多肽，很难利用传统的“从头测序”(de novo sequencing)方法进行测序，一方面，由于含有较多氨基酸，得到的串级质谱图往往碎片信息不完整，对谱峰归属造成很大困难，另一方面即使获得了较为完整的串级质谱图，实验室的服务器电脑无法对如此复杂的碎片峰进行合理归纳，往往会造成电脑超负荷运算陷入死循环。本章不仅利用串级质谱图成功鉴定了一种人工合成寡肽(28个氨基酸)的一级结构，并且详细考察了不同类型质谱仪器、不同碎裂方式、不同碎裂能量、不同激光能量、不同分析软件对于测
序结果的影响，讨论了含有超过20个氨基酸片断的多肽获得合格串级质谱的条件，也为蛋白质组学研究工作如何制定有效的串级质谱策略提供了有力参考。
第六章主要阐述了作为高效液相色谱检测器的四极杆——飞行时间质谱仪(Q-TOF-MS)的研制工作。我们使用三组功能不同的四极杆调制和传输离子，采用正负双脉冲推斥和离子垂直引入的方式将离子束引入到经过优化设计的二级有网式反射器，配合新颖的MCP安装方法和离子检测技术，并使用先进的三级真空系统，最终实现了高灵敏度以及FWHM=11000的高分辨。
The main contributions of this dissertation for the degree of doctor of philosophy are listed as followed, Carrying out many exciting discoveries and inventions of the enrichment and desalting of low-abundance proteins and peptides in proteomics research; Novel one-step on-plate desalting and enrichment protocol for low-abundance proteins by using multifunctional hydrophobic polymer micro-contact-printing; On-plate enrichment and desalting method of low-abundance phosphopeptides for direct MALDI-TOF MS analysis by using cationic polymer and above "one-step desalting" system; Fast and effective enrichment of low-abundance proteins based on combined nano-materials; Development of high-resolution ESI-Q-TOF-MS used as the sensitive and efficient detector of HPLC .
Proteomics — one of the most important fields in the life sciences during the post-genome era— has burst onto the scientific scene with stunning rapidity over the past few years. Proteomics has also become the frontal discipline of analytical chemistry. Proteomics refers to the analysis of all the proteins expressed in a cell or a tissue. The works on proteomics include the characteristics and abundance studies for proteins to find out their functions and locate the key protein which is related to the disease. By studying global patterns of protein abundance and activity and how these change during development or in response to disease, proteomics research has boosted our understanding of systematical cellular behaviour and mechanism of disease. In addition, proteomics benefits the identification of new drug targets and the development of new diagnostic markers in clinical research. Recently proteomics have been obtained many significant achievements in the studies of generation and evolvement of the diseases.
The rapid development of proteomics relies on the advances in the high throughput analytical technologies including biological mass spectrometry (Bio-MS), multi-dimensional separation, and bioinformatics. MALDI and Electrospay —the soft ionizations—have been the key techniques of Bio-MS and applied to the proteomics research. Identification of all proteins in a cell or a tissue and their
locations in the organism and finding out the key proteins by comparative proteomics has made Bio-MS become the critical tool in proteomics study. Many countries have made a large investment in proteomics and the accomplishment of proteomics would play a significant role in finding out drugs and curing diseases.
The work of this doctoral dissertation was mainly accomplished in the Bio-MS laboratory of Department of Chemistry and the Research Center for Proteome of Institutes of Biomedical Sciences of Fudan University. Because the conventional Bio-MS technique platform was difficult for the detection of low-abundance proteins of proteome, the related studies of new technologies and methods become more and more important. Therefore, this dissertation studied on how to enrich and desalt low-abundance proteins effectively and develop some novel strategies: one-step on-plate desalting and enrichment method for low-abundance proteins, on-plate enrichment and desalting of low-abundance phosphopeptides for direct MALDI-TOF MS analysis, fast and effective enrichment of low-abundance proteins depending on combined nano-materials. Since the successful tandem mass spectrometry is very important for the identification of proteins, this dissertation described the whole sequencing process for one synthetic complicated polypeptide composed of 28 amino acids successfully and established a good supplementary method of peptides sequencing for proteomics research. In addition, this dissertation developed high-resolution TOF-MS used as the detector of HPLC.
This doctoral dissertation consists of six parts and the contents are summarized as follows:
In the first chapter, as the key technique in the proteomics study, Bio-MS and its related techniques and applications in the proteomics have been reviewed. Bio-MS becomes more and more important in proteomics with the development of the two soft ionization techniques namely ESI and MALDI, with the improvement of the mass analyzer, with the hybrid of HPLC and CE, with the development of the micro-electrospay and nano-electrospay, as well as the application of tagging by stable isotope. The Bio-MS technique is a definitely powerful tool for the study of the dynamic process of protein-protein reaction, the structure of genetic product, proteins related to diseases and functional protein. As a fresh discipline, the development of proteomics also depends on the newest technical development such as 2DE, chromatography, protein chip, Yeast two-hybrid system, tandem affinity purification,
and so on. The analysis of low abundance proteins has been proved to be a difficult problem since there is no enough technique for the signal amplification of these proteins. Therefore, the isolation and enrichment protocols for low abundance proteins are desirable in proteome research. So a review of the analytical technologies for low-abundance proteins was presented and the investigative direction and purpose of this dissertation were also put forward.
The research works described in the second chapter centers on a novel method of one-step on-plate desalting and low-abundance peptides concentration. A novel micro-contact-printing protocol of multifunctional hydrophobic polymer has been developed for 2DE-MALDI-MS, which can achieve one-step on-plate desalting and analyte concentration. The polymers of PMMA, PMMA-C60, PST and PST-C60 are applied successfully as the MALDI coating materials in the first time. The one-step preparation protocol has a unique and ingenious feature which using "outward-flow" for the separation of analytes from salts. The new micro-contact-printing method of hydrophobic polymers permits analyte to be concentrated on the center of MALDI spot, and meanwhile allows salts to be separated and removed toward the outside of MALDI spot. The on-plate desalting process can be accomplished only for one step without any excessive washing procedure such that the new protocol would provide a potential route to solve the identification problem of low-abundance protein. Normally, the process for proteins digested and transformed from a gel spot to the MALDI target needs a number of steps including protein digestion, peptide extraction, desalting and washing, so low-abundance protein might be easily lost during all these steps. It is expected that the new protocol of hydrophobic polymer micro-contact-printing can effectively reduce the losing of peptides because of the on-spot desalting. The high through-put experiment by using this on-spot desalting strategy is currently on the way in our laboratory.
For the works mentioned in the third chapter, on-plate enrichment and desalting method of low-abundance phosphopeptides for direct MALDI-TOF MS analysis is well tried. Phosphorylation, the most important and ubiquitous post-translational modification of proteins, is able to regulate almost all aspects of cell life in both prokaryotes and eukaryotes. Widespread interest in protein phosphorylation has led to the development of methods to map phosphorylation sites of proteins. The existing preferred approach for phosphorylation site mapping mainly relies on the use of tandem mass spectrometry to sequence individual peptides after proteolysis. However,
this method still remains challenging because the signals for phosphorylated peptides are strongly suppressed by other abundant unphosphorylated peptides contained in protein digests during positive mass spectrometric analysis. Therefore, the separation and enrichment of phosphorylated peptides from unphosphorylated ones is highly desirable. At present, one solution to this problem for proteomics research is to carry out HPLC separation of the phosphopeptides from the other peptides prior to mass spectrometric analysis. Immobilized metal ion affinity chromatography (IMAC) has been often used for the selective enrichment of phosphopeptides from proteolytic digest mixtures. However, chromatography introduces additional sample handling and preparation time prior to MALDI or electrospray mass spectrometry. In this chapter, we reported a solution to the problem of the suppression of phosphorylated peptides during positive ion MALDI-TOF-MS by using the cationic-polymer coating plate combined with the "One-step desalting" system. This cationic-polymer coating can efficiently enriches the phosphopeptides and improves the sensitivity of the MS devices, Meanwhile it also eliminates the interference of the salts on the plate which would simplify the procedure of sample concentration and desalting.
In the fourth chapter, the development of a particle-free MALDI and " octopus-like" enrichment protocol is mentioned. In this protocol, we select nanoparticles of calcium carbonate derivatized with poly(methyl methacrylate) (PMMA) because of its ability to adsorb the peptide/protein. The particle denoted as CaCO_3 - PMMA has a destroyable core of CaCO_3, which can be removed later for a particle-free MALDI analysis. When the CaCO_3 - PMMA material is added dropwise to the sample solution, the linear chains of PMMA linked on the CaCO_3 core will be flexible and spread out into the solution like the tentacles of an octopus. Not only the CaCO_3 - PMMA nanoparticles are applied for the first time for the enrichment of low-abundance peptides and proteins, but also the process of enrichment is very quick and efficient. The resulting nanoparticle-adsorbed peptides or proteins can be analyzed by MALDI-TOF MS in the particle-free mode with high reproducibility and good recovery, thereby avoiding sample loss and contamination inside the mass spectrometer. It has been found that CaCO_3 - PMMA nanoparticles exhibit a strong enriching and desalting ability, which could pave way to novel approach to the enrichment of trace-level proteins or peptides, as well as new applications for CaCO_3 - PMMA nanoparticles.
One synthetic complicated polypeptide composed of 28 amino acids was
successfully sequenced by MALDI-MSMS (CID) and ESI-MSMS (CID) in the fifth study. I obtained the perfect tandem mass spectrum consisting full product ions of b and y by investigating the parameters of mass spectrometry instruments, such as the intensity of Laser, the energy of CID, the difference of sequencing software. et al. Results indicate that this method can effectively solve the difficulty occurring in de novo sequencing, such as dead-response of computer. The established method is a good supplement for peptides sequencing and the discussion of various parameters is important for the establishment of tandem mass spectrometry proocol in proteomics research work.
In the last chapter, two ESI-Triple Quadrupole-Orthogonal Acceleration-Reflecting-TOF mass spectrometer analytical systems are successfully developed, which are equipped with electrospray ionization source which could be directly connected with HPLC as an outstanding detector. The ESI-QQQ-TOF mass spectrometers have some promising features, such as an ESI source with heatable nebulizer settled on a smart triaxially moving stage, an excellent ion-optics system composed with triple-quadruple, double-pulse acceleration, and a double stage reflector with homemade grids. The Gramicidin-S sample concentration below to 3 fmol/μL can be identified by these instruments under the optimized conditions. The mass range of these instruments is from 50 to 6000 u with a general ESI interface to the HPLC. The optimal mass resolution exceeds 11000 (Full Width at Half Maximum, FWHM) and the signal/noise ratio of reserpine (10 pg/μL) is greater than 100. We hope the homemade Q-TOF-MS would be widely used in protein chemistry and proteomics research due to its high sensitivity, high resolution and high accuracy.
Flow”过程结合自制的多功能疏水性聚合物成功实现了一步高效靶上除盐与样品富集直接MALDI-MS分析，并成功应用到实际样品的蛋白质组学研究中；同时利用上述体系，使用阳离子型聚合物成功实现了对低丰度磷酸化肽段的靶上富集与除盐；首次利用聚合物-无机纳米复合材料成功实现了低丰度蛋白质／多肽的高效、快速和高回收率富集；参与研制成功了作为高效液相色谱检测器的电喷雾—四极杆—飞行时间质谱仪(ESI-Q-TOF-MS)，填补了国内空白。
蛋白质组学作为后基因组时代生命科学领域的热点，近年来得到了蓬勃的发展，已涉足生命科学中一系列前沿领域，并成为分析化学研究领域的最前沿课题。它的内容包括分离和分析细胞与组织的全部蛋白并直接找到一组或几组功能蛋白，研究它们与功能基因(组)的内在联系。蛋白质组研究具有观察由多基因事件引起的多蛋白质组分整体变化的独特优势，更接近生命现象的本质，在药靶研究中具有潜在价值，可通过对蛋白质性质、丰度的考察来揭示它的功能，进而找到与人类重大疾病相关的差异蛋白，使之成为诊断、治疗及药物筛选的靶分子。目前蛋白质组已被广泛用于研究各种疾病的发生、发展规律，并取得了很多重大的成就。
蛋白质组学的科学研究之所以能够取得蓬勃的发展，主要依赖于生物质谱技术的飞速发展以及高通量分离和分析技术的突破性进步。首先是质谱技术尤其是“软电离源”技术——电喷雾和基质辅助激光解析离子源的发展，使之成为检测微量甚至是痕量蛋白质分子的重要手段。高通量、高效的分离技术和大规模、高效率、高准确性地鉴定一个组织或细胞乃至亚细胞中的全部蛋白质以及利用稳定同位素标记方式与多维分离-串级质谱实现大规模的蛋白质定量分析也已经使得生物质谱成为实现这一目标的核心分析技术。生物信息学的建立形成了国际性的科学大协作。目前，世界各主要国家都不惜巨资进行蛋白质组的研究。蛋白质组学研究的进一步深入，将对了解疾病的发生和药物的筛选起到决定性的作用。
本博士学位论文工作主要是在化学系生物质谱实验室和生物医学研究院蛋白质组学研究中心完成的。由于传统的生物质谱技术平台已不足以应对蛋白质组学中低丰度蛋白检测的要求，所以研究和发展针对低丰度蛋白检测方面的新技术
与新方法尤显得意义重大，本论文以此为切入点，研究了蛋白质组学分析中如何实现低丰度蛋白有效富集和除盐的问题，包括：利用疏水性聚合物微印迹技术实现的靶上一步除盐和样品富集技术；开展了靶上磷酸化肽段直接浓缩与除盐技术的研究；发展了利用聚合物-无机纳米复合材料实现的低丰度蛋白快速高效富集技术。又因为串级质谱的成功鉴定对于蛋白质组学研究也非常重要，所以本论文以一种含有多达28个氨基酸的复杂多肽为对象研究了如何对大质量多肽进行有效的串级质谱全序列分析；本论文作者还参与研制成功了作为高效液相色谱检测器的高分辩飞行时间质谱仪。
本论文共分六章，主要内容摘要如下：
第一章主要综述了蛋白质组学研究中的关键技术——生物质谱相关技术的发展及其在蛋白质组学中的应用。新的“软电离”方式——基质辅助激光解吸电离技术(MALDI)和电喷雾电离技术(ESI)的问世、质谱质量分析器的改善、各种分离技术如高效液相色谱／毛细管电泳等和质谱的联用、稳定同位素标记技术的发展及应用，使得生物质谱已成为蛋白质组学研究中无可替代的核心技术平台。生物质谱在对基因工程产物、功能蛋白及疾病相关蛋白的定性、定量分析中具有无可比拟的优越性，在蛋白的相互作用、蛋白质的折叠等动力学过程的研究中具有极大的潜力。而蛋白质组学作为一门新兴学科，它的发展现状和最新技术进展还包括双向凝胶电泳技术、色谱分离技术、蛋白质芯片技术、酵母双杂交技术和串联亲和纯化技术等。低丰度蛋白的分析与鉴定是蛋白质组学研究的重点和难点内容之一，在生物体中承担重要生命活动的蛋白往往都是低丰度蛋白，然而其极低的含量给后续的分析和检测带来困难，限制了人们对它们的研究和认识，因此低丰度蛋白的有效浓缩与除盐是实现其准确分析和鉴定的重要条件，所以本章还综述了目前针对低丰度蛋白检测的技术，并提出了本课题工作的研究方向。
第二章研究工作主要涉及关于低丰度蛋白靶上一步除盐与富集直接MALDI-MS分析的新方法。这部分工作是通过将疏水性聚合物微印迹技术与基质辅助激光解析离子化质谱联用，巧妙利用液滴内部的“Outward Flow”效应，结合自制的多功能疏水性聚合物成功实现了痕量多肽的靶上一步除盐与富集。微印迹的疏水性聚合物对蛋白质和多肽有很好的吸附富集效果，但是对无机盐和其他污染物吸附很少，利用固体表面液珠蒸发过程中的外流作用，被疏水性聚合物吸附的样品无需额外的洗脱除盐步骤就可实现一步除盐并可直接进行MALDI-TOF-MS分析。本方法不仅成功实现了样品一步除盐与富集的特性，而且具有灵敏度高、重现性高、通量高、耐盐能力强、经济和省时等特点。可广泛用于蛋白质组学领域，大大拓展了疏水性聚合物的应用范围。此工作已显现出比传
统商业Ziptip或ZipPlate除盐、富集系统更优秀的特性，并成功应用在我们课题组承担的国际人类蛋白质组人肝计划和中国人肝计划。
第三章主要阐述了低丰度磷酸化肽段靶上浓缩与除盐—直接MALDI-MS分析的研究。蛋白质的翻译后修饰是目前蛋白质组研究中的一个重要课题，目前蛋白质组技术研究的主要目标之一是建立一套能快速、有效、高通量地分析鉴定发生翻译后修饰的蛋白质的方法技术。而蛋白质磷酸化是最常见、最重要的一种蛋白翻译后修饰方式。蛋白质磷酸化和去磷酸化几乎调节着生命活动的整个过程，包括细胞的增殖、发育和分化、神经活动、肌肉收缩、新陈代谢、肿瘤发生等。目前蛋白质组学方法中磷酸化蛋白、肽段的富集技术主要包括双向磷酸多肽谱图法、高分辨率的凝胶电泳法(2DE)、反相高效液相色谱法、固定化金属亲和色谱(IMAC)、抗体富集、化学标记富集等。磷酸化肽段的质谱检测难点主要在于其丰度低、动态的体内磷酸化过程、难于离子化、受其它高丰度的非磷酸化肽段信号的强烈抑制等原因。本论文采用一种阳离子性聚合物材料，结合第二章介绍的一步除盐与样品富集体系，在靶上有效富集了低浓度磷酸化肽段，大大简化了样品富集步骤。本方法可检测到10fmol／μL β-酪蛋白中的单磷酸化肽，并可得到很好的串级质谱信息。
第四章研究工作主要涉及一种以纳米碳酸钙球表面原位聚合聚甲基丙烯酸甲酯组合材料(简称CaCO_3-PMMA)作为纳米吸附剂，进行痕量肽及蛋白样品的富集——伴随无固态颗粒化基质辅助激光解析离子源质谱直接分析的方法。此聚合物-无机纳米复合材料可对蛋白质和多肽进行快速高效富集，与基质辅助激光解吸离子源质谱有很好的相容性，吸附了样品的CaCO_3-PMMA在进入质谱分析前被巧妙的去核——从而避免固体颗粒对信号重现性的影响及其溅射对质谱仪器的损害。本方法操作简单，快速高效，既避免了常规吹干富集方法的样品损失问题，又具有很好的耐盐性。本方法可广泛适用于蛋白质组学相关领域，并大大拓展了聚合物-无机纳米复合材料CaCO_3-PMMA的应用范围。
第五章主要介绍了对含有28个氨基酸的复杂多肽的串级质谱全序列分析研究。对于含有太多氨基酸片断(大于20个)的多肽，很难利用传统的“从头测序”(de novo sequencing)方法进行测序，一方面，由于含有较多氨基酸，得到的串级质谱图往往碎片信息不完整，对谱峰归属造成很大困难，另一方面即使获得了较为完整的串级质谱图，实验室的服务器电脑无法对如此复杂的碎片峰进行合理归纳，往往会造成电脑超负荷运算陷入死循环。本章不仅利用串级质谱图成功鉴定了一种人工合成寡肽(28个氨基酸)的一级结构，并且详细考察了不同类型质谱仪器、不同碎裂方式、不同碎裂能量、不同激光能量、不同分析软件对于测
序结果的影响，讨论了含有超过20个氨基酸片断的多肽获得合格串级质谱的条件，也为蛋白质组学研究工作如何制定有效的串级质谱策略提供了有力参考。
第六章主要阐述了作为高效液相色谱检测器的四极杆——飞行时间质谱仪(Q-TOF-MS)的研制工作。我们使用三组功能不同的四极杆调制和传输离子，采用正负双脉冲推斥和离子垂直引入的方式将离子束引入到经过优化设计的二级有网式反射器，配合新颖的MCP安装方法和离子检测技术，并使用先进的三级真空系统，最终实现了高灵敏度以及FWHM=11000的高分辨。
The main contributions of this dissertation for the degree of doctor of philosophy are listed as followed, Carrying out many exciting discoveries and inventions of the enrichment and desalting of low-abundance proteins and peptides in proteomics research; Novel one-step on-plate desalting and enrichment protocol for low-abundance proteins by using multifunctional hydrophobic polymer micro-contact-printing; On-plate enrichment and desalting method of low-abundance phosphopeptides for direct MALDI-TOF MS analysis by using cationic polymer and above "one-step desalting" system; Fast and effective enrichment of low-abundance proteins based on combined nano-materials; Development of high-resolution ESI-Q-TOF-MS used as the sensitive and efficient detector of HPLC .
Proteomics — one of the most important fields in the life sciences during the post-genome era— has burst onto the scientific scene with stunning rapidity over the past few years. Proteomics has also become the frontal discipline of analytical chemistry. Proteomics refers to the analysis of all the proteins expressed in a cell or a tissue. The works on proteomics include the characteristics and abundance studies for proteins to find out their functions and locate the key protein which is related to the disease. By studying global patterns of protein abundance and activity and how these change during development or in response to disease, proteomics research has boosted our understanding of systematical cellular behaviour and mechanism of disease. In addition, proteomics benefits the identification of new drug targets and the development of new diagnostic markers in clinical research. Recently proteomics have been obtained many significant achievements in the studies of generation and evolvement of the diseases.
The rapid development of proteomics relies on the advances in the high throughput analytical technologies including biological mass spectrometry (Bio-MS), multi-dimensional separation, and bioinformatics. MALDI and Electrospay —the soft ionizations—have been the key techniques of Bio-MS and applied to the proteomics research. Identification of all proteins in a cell or a tissue and their
locations in the organism and finding out the key proteins by comparative proteomics has made Bio-MS become the critical tool in proteomics study. Many countries have made a large investment in proteomics and the accomplishment of proteomics would play a significant role in finding out drugs and curing diseases.
The work of this doctoral dissertation was mainly accomplished in the Bio-MS laboratory of Department of Chemistry and the Research Center for Proteome of Institutes of Biomedical Sciences of Fudan University. Because the conventional Bio-MS technique platform was difficult for the detection of low-abundance proteins of proteome, the related studies of new technologies and methods become more and more important. Therefore, this dissertation studied on how to enrich and desalt low-abundance proteins effectively and develop some novel strategies: one-step on-plate desalting and enrichment method for low-abundance proteins, on-plate enrichment and desalting of low-abundance phosphopeptides for direct MALDI-TOF MS analysis, fast and effective enrichment of low-abundance proteins depending on combined nano-materials. Since the successful tandem mass spectrometry is very important for the identification of proteins, this dissertation described the whole sequencing process for one synthetic complicated polypeptide composed of 28 amino acids successfully and established a good supplementary method of peptides sequencing for proteomics research. In addition, this dissertation developed high-resolution TOF-MS used as the detector of HPLC.
This doctoral dissertation consists of six parts and the contents are summarized as follows:
In the first chapter, as the key technique in the proteomics study, Bio-MS and its related techniques and applications in the proteomics have been reviewed. Bio-MS becomes more and more important in proteomics with the development of the two soft ionization techniques namely ESI and MALDI, with the improvement of the mass analyzer, with the hybrid of HPLC and CE, with the development of the micro-electrospay and nano-electrospay, as well as the application of tagging by stable isotope. The Bio-MS technique is a definitely powerful tool for the study of the dynamic process of protein-protein reaction, the structure of genetic product, proteins related to diseases and functional protein. As a fresh discipline, the development of proteomics also depends on the newest technical development such as 2DE, chromatography, protein chip, Yeast two-hybrid system, tandem affinity purification,
and so on. The analysis of low abundance proteins has been proved to be a difficult problem since there is no enough technique for the signal amplification of these proteins. Therefore, the isolation and enrichment protocols for low abundance proteins are desirable in proteome research. So a review of the analytical technologies for low-abundance proteins was presented and the investigative direction and purpose of this dissertation were also put forward.
The research works described in the second chapter centers on a novel method of one-step on-plate desalting and low-abundance peptides concentration. A novel micro-contact-printing protocol of multifunctional hydrophobic polymer has been developed for 2DE-MALDI-MS, which can achieve one-step on-plate desalting and analyte concentration. The polymers of PMMA, PMMA-C60, PST and PST-C60 are applied successfully as the MALDI coating materials in the first time. The one-step preparation protocol has a unique and ingenious feature which using "outward-flow" for the separation of analytes from salts. The new micro-contact-printing method of hydrophobic polymers permits analyte to be concentrated on the center of MALDI spot, and meanwhile allows salts to be separated and removed toward the outside of MALDI spot. The on-plate desalting process can be accomplished only for one step without any excessive washing procedure such that the new protocol would provide a potential route to solve the identification problem of low-abundance protein. Normally, the process for proteins digested and transformed from a gel spot to the MALDI target needs a number of steps including protein digestion, peptide extraction, desalting and washing, so low-abundance protein might be easily lost during all these steps. It is expected that the new protocol of hydrophobic polymer micro-contact-printing can effectively reduce the losing of peptides because of the on-spot desalting. The high through-put experiment by using this on-spot desalting strategy is currently on the way in our laboratory.
For the works mentioned in the third chapter, on-plate enrichment and desalting method of low-abundance phosphopeptides for direct MALDI-TOF MS analysis is well tried. Phosphorylation, the most important and ubiquitous post-translational modification of proteins, is able to regulate almost all aspects of cell life in both prokaryotes and eukaryotes. Widespread interest in protein phosphorylation has led to the development of methods to map phosphorylation sites of proteins. The existing preferred approach for phosphorylation site mapping mainly relies on the use of tandem mass spectrometry to sequence individual peptides after proteolysis. However,
this method still remains challenging because the signals for phosphorylated peptides are strongly suppressed by other abundant unphosphorylated peptides contained in protein digests during positive mass spectrometric analysis. Therefore, the separation and enrichment of phosphorylated peptides from unphosphorylated ones is highly desirable. At present, one solution to this problem for proteomics research is to carry out HPLC separation of the phosphopeptides from the other peptides prior to mass spectrometric analysis. Immobilized metal ion affinity chromatography (IMAC) has been often used for the selective enrichment of phosphopeptides from proteolytic digest mixtures. However, chromatography introduces additional sample handling and preparation time prior to MALDI or electrospray mass spectrometry. In this chapter, we reported a solution to the problem of the suppression of phosphorylated peptides during positive ion MALDI-TOF-MS by using the cationic-polymer coating plate combined with the "One-step desalting" system. This cationic-polymer coating can efficiently enriches the phosphopeptides and improves the sensitivity of the MS devices, Meanwhile it also eliminates the interference of the salts on the plate which would simplify the procedure of sample concentration and desalting.
In the fourth chapter, the development of a particle-free MALDI and " octopus-like" enrichment protocol is mentioned. In this protocol, we select nanoparticles of calcium carbonate derivatized with poly(methyl methacrylate) (PMMA) because of its ability to adsorb the peptide/protein. The particle denoted as CaCO_3 - PMMA has a destroyable core of CaCO_3, which can be removed later for a particle-free MALDI analysis. When the CaCO_3 - PMMA material is added dropwise to the sample solution, the linear chains of PMMA linked on the CaCO_3 core will be flexible and spread out into the solution like the tentacles of an octopus. Not only the CaCO_3 - PMMA nanoparticles are applied for the first time for the enrichment of low-abundance peptides and proteins, but also the process of enrichment is very quick and efficient. The resulting nanoparticle-adsorbed peptides or proteins can be analyzed by MALDI-TOF MS in the particle-free mode with high reproducibility and good recovery, thereby avoiding sample loss and contamination inside the mass spectrometer. It has been found that CaCO_3 - PMMA nanoparticles exhibit a strong enriching and desalting ability, which could pave way to novel approach to the enrichment of trace-level proteins or peptides, as well as new applications for CaCO_3 - PMMA nanoparticles.
One synthetic complicated polypeptide composed of 28 amino acids was
successfully sequenced by MALDI-MSMS (CID) and ESI-MSMS (CID) in the fifth study. I obtained the perfect tandem mass spectrum consisting full product ions of b and y by investigating the parameters of mass spectrometry instruments, such as the intensity of Laser, the energy of CID, the difference of sequencing software. et al. Results indicate that this method can effectively solve the difficulty occurring in de novo sequencing, such as dead-response of computer. The established method is a good supplement for peptides sequencing and the discussion of various parameters is important for the establishment of tandem mass spectrometry proocol in proteomics research work.
In the last chapter, two ESI-Triple Quadrupole-Orthogonal Acceleration-Reflecting-TOF mass spectrometer analytical systems are successfully developed, which are equipped with electrospray ionization source which could be directly connected with HPLC as an outstanding detector. The ESI-QQQ-TOF mass spectrometers have some promising features, such as an ESI source with heatable nebulizer settled on a smart triaxially moving stage, an excellent ion-optics system composed with triple-quadruple, double-pulse acceleration, and a double stage reflector with homemade grids. The Gramicidin-S sample concentration below to 3 fmol/μL can be identified by these instruments under the optimized conditions. The mass range of these instruments is from 50 to 6000 u with a general ESI interface to the HPLC. The optimal mass resolution exceeds 11000 (Full Width at Half Maximum, FWHM) and the signal/noise ratio of reserpine (10 pg/μL) is greater than 100. We hope the homemade Q-TOF-MS would be widely used in protein chemistry and proteomics research due to its high sensitivity, high resolution and high accuracy.
引文
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