高丰度蛋白质的除去及蛋白质的多维色谱分离与定量新方法研究
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摘要
20世纪中期以来，随着DNA双螺旋结构的提出和蛋白质空间结构的X射线解析，开始了分子生物学时代，对遗传信息载体DNA和生命功能的主要体现者蛋白质的研究，成为生命科学研究的主要内容。90年代中期，在人类基因组计划(Human Genomic Project)研究发展及功能基因组学的基础上，国际上萌发产生了一门在整体水平上研究细胞内蛋白质的组成及其活动规律的新兴学科——蛋白质组学(Proteomics)，它以蛋白质组(Proteome)为研究对象。蛋白质组学(proteomics)已经成为功能基因组学研究的重要领域，其重要性和战略意义日益显著。
蛋白质组学研究主要有两种路线：第一种是传统的双向凝胶电泳(2-DE)分离技术。但是双向凝胶电泳技术仍然存在许多不足和一些难以克服的缺陷，比如有限的动态范围，分离样品中分子量差别较大的蛋白、低拷贝蛋白、疏水蛋白以及极酸极碱蛋白的分辨能力比较差，而且其操作过程费时费力，自动化程度低。针对这些固有的技术上的缺陷，具有快速，高效，自动化程度高等优点的液相色谱技术得到了长足发展，并成为蛋白质组学研究的第二条技术路线。发展两维乃至多维色谱分离技术，提高峰容量和分离能力是根本上解决复杂样品分离问题的方法。从理论上说，只要组合在一起的两种模式的分离机理正交，整个二维系统的峰容量是每一维峰容量的乘积，特别适合于复杂样品的分析。在过去的十几年中，已经出现了一些被认为是突破性的进展，Jorgenson(多维色谱-电泳技术)，Yates(Shot-gun技术)，Aebersold(ICAT技术)等科学家在蛋白质组学新方法的研究方面打开了一个崭新的局面。
目前，蛋白质组学面临的两大挑战是高丰度蛋白质压制低丰度蛋白质造成低丰度蛋白质检测困难以及蛋白质的定量问题。Shot-gun为代表的bottom-up技术在分离之前将蛋白质样品进行酶解，一个蛋白质酶解成多个肽段，这势必使原本就很复杂的样品变得更加复杂，不仅给色谱的分离能力与质谱的扫描速度提出挑战，不利于低丰度蛋白质的检测，而且将蛋白质酶解成肽段的同时又损失了完整蛋白质的信息。ICAT技术在蛋白质的相对定量方面发挥了重大作用，然而已有的定量技术仅局限在相对定量方面。因此，现有的多维色谱技术在解决蛋白质组学的两大问题上存在许多不足，本论文就是围绕当前蛋白质组学研究中存在的问题开展工作的，建立发展多维色谱技术方法达到实现高丰度蛋白质的去除以及完整蛋白质的分离鉴定以及定量等目的。
本论文共分五章。主要内容摘要如下：
第一章总结了蛋白质组学的现状与发展以及多维色谱与其相关技术在蛋白质组学中的应用与进展。介绍了二维／多维分离方法的理论依据，探讨了目前蛋白质组学研究使用的技术模式的成功与不足。并介绍了本论文选题的目的和意义，着重在于如何利用多维液相色谱的技术实现在完整蛋白水平上的分离，去除高丰度蛋白质以及利用多维液相色谱技术同时实现对蛋白质的定性定量等问题。
第二章以鼠肝为研究对象比较了不同的提取环境对动物组织中蛋白质提取的影响。主要研究了三种提取环境：酸性、中性和碱性环境。利用双向凝胶电泳分离成像技术比较了在三种不同环境下提取的蛋白质的分布的差异性，通过实验证明了在不同的提取环境下提取的蛋白质在种类和含量上都是不同的，同时也证明了在蛋白质组学的研究中不同的分离路线或分离模式应该根据具体分离条件的酸碱度的不同选用不同的蛋白提取方法，以避免在分离的过程中因沉淀问题而损失蛋白质，为后续工作打下基础。
第三章针对肝脏组织蛋白建立了反相高效液相色谱／双向凝胶电泳(RPLC／2-DE)的三维分离系统。2-DE技术是比较成熟的蛋白质分离手段，但是样品负载量低是影响中低丰度蛋白检测的一个重要原因，同时2-DE技术对于复杂的蛋白质样品的分离能力是有限的。RPLC是生物分析中常用的高效的分离模式，对蛋白或肽等有很好的分离能力，还具有除盐纯化样品的能力。RPLC与2-DE的分离机理正交，两种技术联合使用能在很大程度上提高样品的分辨率。本章工作以大鼠的肝脏组织蛋白为研究对象建立了实验路线并确立了实验条件。研究表明，蛋白质样品经过RPLC预分离之后，不同的蛋白就被富集浓缩到不同的馏份中，极大的提高了单个馏份中的蛋白在2-DE上的上样量和分辨率，这一点在凝胶扫描图上可以直观的反映出来，同时，实验证明RPLC分离蛋白质有着很好的重现性，据此可以对同一样品进行平行收集，以达到进一步增大单个馏份中蛋白的上样量的目的。因此，将RPLC作为预分离手段用于2-DE之前对样品进行预分离可以提高蛋白质在2-DE上的上样量和分辨率。这条技术路线已经在中国人肝项目表达谱的研究中得到应用。
第四章直接采用多维液相色谱的方法通过多维色谱分离的手段去除生物样品中的高丰度蛋白。中心思路就是：首先利用多维色谱技术对蛋白样品进行有效分离，在完整蛋白分离的基础上，将高丰度蛋白质在酶解成更复杂的肽段之前除掉。这条技术路线目前还没有类似报道。具体路线简述如下：
发展了强阳离子交换色谱／反相高效液相色谱(SCX／RPLC)分离系统，对鼠肝组织蛋白进行高效的分离。使用连续地线性盐梯度将蛋白质从SCX色谱柱上洗脱下来，得到62个馏份，每个馏份进一步使用常规的RPLC进行第二维地分离，整个分离过程使用紫外信号对蛋白的色谱峰进行监测，在第二维的分离过程中将信号强也就是量大的高丰度蛋白单独收集，其余中低丰度的蛋白进行合并、浓缩和酶解，然后使用毛细管反相色谱(cRPLC)进行分离，之后进行质谱鉴定，62个馏份分别如法炮制。结果表明，一次实验流程可以去除77个高丰度蛋白，占总蛋白量的34.5％，与不经过去除高丰度蛋白的样品进行比较，鉴定蛋白的数量提高了2到3倍之多。
在此基础上，我们进一步简化实验路线并提高方法地通量。来自SCX分离之后的62个馏份经过RPLC进一步分离之后，我们将所有含有中低丰度蛋白的洗脱液合并浓缩到一起，共同酶解之后使用在线的二维分离系统，即shot-gun技术对酶解之后的肽段进行分析鉴定。简化后的实验路线对中国人肝样品进行了分析，58个高丰度蛋白质被去除，共鉴定出1213个蛋白质。
总之，这套系统对降低蛋白质样品地复杂性，避免高丰度蛋白质在分离和质谱鉴定过程中压制中低丰度蛋白提供了一个新的手段和思路。另外，通过多维液相色谱分离的方法去除高丰度蛋白质，相对通常使用的免疫亲和的手段，无疑更具有通用性、灵活性、低成本和周期短的优势。
第五章发展了多维液相色谱的Top-down技术路线，即SCX／cRPLC／靶上酶解／MALDI-TOF-TOF分离鉴定系统。采用SCX／cRPLC分离系统，实现了在完整蛋白水平上的两维分离，本实验室发展的新方法靶上酶解技术的采用将蛋白质分离与质谱鉴定有效的结合起来，从而实现了蛋白从分离、酶解到鉴定这样一个完整的Top-down路线。蛋白质样品经过常规柱SCX分离之后，得到62个馏份，每个馏份继续使用毛细管反相柱cRPLC进行第二维分离，cRPLC作为第二维具有除盐和纯化样品的作用，为直接酶解提供了可能，利用自动点样仪将经过cRPLC的洗脱液直接收集到标准的MALDI靶板上，点样频率为30秒／个，经过靶上单点酶解之后用MALDI-TOF-TOF鉴定。整个系统对中国人肝蛋白进行了鉴定，共鉴定出3313个唯一蛋白。
与通常采用的shot-gun技术相比，我们发展的多维液相色谱的Top-down技术路线更能充分的分离蛋白质，得到更多的包括肽谱和疏水性等有关蛋白质的信息。与2-DE相比具有成本低和自动化高等优势。
在此基础上，我们进一步发展为三维蛋白分离系统，即SEC／SCX／RPLC系统，对肝脏蛋白进行更为完全的分离，利用紫外可见检测对蛋白峰进行归一化处理，进一步计算出蛋白的含量，相对应的蛋白质色谱峰同时进行浓缩、酶解、进而MALDI-TOF-TOF检测定性分析，以达到对单个蛋白同时进行定性和定量的目的。这条路线已经进行了有成效的探索，得到一些初步的结果，为蛋白质组学中的定量问题提供了一个可行的有价值的新思路。
总之，本论文围绕蛋白质组学的研究热点，以液相色谱分离系统为基础，发展了多种有效的分离系统，以完整蛋白质的分离为指导思想，建立了反相色谱预分离结合双向凝胶电泳的分离路线；开创了基于多维色谱分离为基础的高丰度蛋白质去除系统；发展了多维液相色谱的Top-down技术路线，试图在蛋白质研究主流的2-DE-MS技术之外，另辟蹊径，对蛋白组学新方法学的建立进行了有益的探索和研究，而且多数实验路线已经在中国人肝项目中投入使用，贡献了大量的有价值的实验数据。
Since 1950's, scientific interest has been increasingly shifting to molecular biology with the accomplishment of the gene sequencing of Human Genome Project (HGP). Proteomics has been the focus due to the role of executor of the life function. Proteomics refers to the analysis of all the proteins expressed in a cell or tissue. The investigation of functional proteome is of great significance given that functions of most of genes are still not well understood. Presently proteomic research focuses on differential proteome analysis of human diseases, which is designed to find key proteins with potentials to be used as markers for diagnosis or targets for medication. Proteomics is also becoming the spotlight of analytical chemistry.
2D PAGE is the most universal method for proteomics and posses high resolve power for proteins. Some problems in 2D PAGE, however, are still difficult to be overcome such as limited pH range, time-consuming and inefficient sensitivity for low abundant proteins. The reality has motivated considerable effort in developing new technique to resolve proteomics as alternative approach to 2D PAGE.
Liquid chromatography technologies are powerful technology to resolve proteins. But conventional one dimensional LC systems are incapable of completely resolving all the components in a complex mixture due to insufficient peak capacity. The development of two-or multi-dimensional column based separation techniques greatly improve the resolve power and peak capacity. During the past decade, a lot of analysts contributed to this field, such as Jorgenson's multi-dimensional separation, Yates' shot-gun technique, Aebersold's ICAT technique and so on.
This dissertation is divided into 6 parts.
In the first chapter, advances in 2D and multidimensional separation techniques were summarized with details. The theory basis of multidimensional separation techniques was introduced and the advantages and shortcomings of existing technical modes were discussed. The intention and meaning of this dissertation were explained.
In chapter 2, we used rat as animal model to compare the effect of different extraction conditions on the extracted proteins. The extract methods of tissue sample at acidic, neutral and basic pH were described and compared by using two-dimensional gel electrophoresis and reversed-phase liquid chromatography. The images on gel and mass spectra showed that the
different method can enrich proteins at different pH range. Different pH extract methods can be applied into corresponding liquid chromatography mode with the compatible mobile phase so that the loss and precipitation could be avoided. The good reproducibility enables the sample preparation methods to be widely applied in proteomics analysis.
In chapter 3, we describe an approach for fractionating complex protein samples from rat liver prior to 2-DE using RPLC. The study indicated that RPLC prefractionation can provide strong enrichment effect which enabled us to visualize additional and less abundance proteins. Chromatographic enrichment was also demonstrated by the peptide mass fingerprint data, which gave mass spectra with increased number of detected peptide and improved signal intensity. The reproducibility of this prefractionation technology allows pooling of several consecutive runs of the same sample, resulting in a highly enrichment of low abundance proteins. This technology route has been applied into the study of profiling mode of Chinese Human Liver Proteomics Project (CHLPP).
In chapter 4, for the first time a comprehensive two-dimensional (2D) liquid-phase separation system, coupling strong cation exchange chromatography (SCX) to reversed-phase high performance liquid chromatography (RPLC), instead of immuno-affinity chromatography, was developed at the intact protein level for depletion of high abundance proteins from rat liver. The core idea was to deplete the high abundance proteins before the digestion.
Proteins bound to the SCX phase were eluted off using a consecutive linear salt gradient. After salt fractionation, 62 fractions were obtained. Every fraction was separated further by RPLC. Ultraviolet signal was used to detect the separation process. The protein peaks with signal intensity above 0.1 AU was defined as high abundance proteins, whereas the other was defined as middle- or low high abundance protein. Then, the effluents contained high abundance proteins were collected individually and other effluents were pooled together. The combined middle- or low high abundance proteins were lyophilized, digested and separated by capillary reversed phase liquid chromatography (cRPLC). Mass spectrometry was used to analyze the protein. 62 fractions were treated using the same method. The results were that 77 high abundance proteins were depleted in an experimental process and identified proteins number was increased 2-3 times.
Based on the results, a simplified rapid-speed and high-throughput protocol was put forward further. Instead of separating every fraction using cRPLC, all effluents containing
middle- or low abundance protein were combined, enriched, digested and separated by online shotgun technology. The simplified method was used to analyze Chinese liver sample. 58 high abundance proteins were depleted and 1213 proteins were identified.
In summery, the system presented a novel idea about the depletion of high abundance proteins. In contrast with affinity technology, this strategy with the advantages of low-cost and saving-time has no bias to any proteins and could realize the global proteins analysis.
In chapter 5, for the first time, the 2-D separation platform based on the liquid chromatography combined with on-probe digestion technique and identification of mass spectrometry was constructed in intact proteins level for separation and identification of complex liver tissue proteins. The 2-D liquid chromatographic system was constructed by coupling SCX with cRPLC. Proteins were prefractionated by SCX according to charge in the first dimensional separation. 62 fractions eluting from the first dimension were subjected automatically to cRPLC to separate similarly charged proteins on the basis of their various hydrophobicities. A novel rapid on-target digestion technique was adopted to couple effectively the separation technique and mass spectrometry technique. After digestion, the matrix was deposited on the same spot, respectively. Then, the dried plate was analyzed by mass spectrometry. This new technology coupled the top-down approach and bottom-up technologies. The high efficiency of system was demonstrated for analysis of intact proteins from the soluble lysates of normal human liver. A total of 3313 proteins were identified.
We further developed three-dimensional separation system combined SEC with the SCX/RPLC mentioned above. This 3D system exhibited the potential of further high resolution for extremely complicated mixture. The intention of 3D system was to realize the identification and quantification of proteins. We had explored some relative experiments and made some effective results.
In a word, the main contributes of this dissertation is the development of effective separation system based multi-dimensional system. We aim at exploring and finding out new technological systems for proteomics, so that more breakthroughs can be obtained at the qualitative analysis and quantification study.
蛋白质组学研究主要有两种路线：第一种是传统的双向凝胶电泳(2-DE)分离技术。但是双向凝胶电泳技术仍然存在许多不足和一些难以克服的缺陷，比如有限的动态范围，分离样品中分子量差别较大的蛋白、低拷贝蛋白、疏水蛋白以及极酸极碱蛋白的分辨能力比较差，而且其操作过程费时费力，自动化程度低。针对这些固有的技术上的缺陷，具有快速，高效，自动化程度高等优点的液相色谱技术得到了长足发展，并成为蛋白质组学研究的第二条技术路线。发展两维乃至多维色谱分离技术，提高峰容量和分离能力是根本上解决复杂样品分离问题的方法。从理论上说，只要组合在一起的两种模式的分离机理正交，整个二维系统的峰容量是每一维峰容量的乘积，特别适合于复杂样品的分析。在过去的十几年中，已经出现了一些被认为是突破性的进展，Jorgenson(多维色谱-电泳技术)，Yates(Shot-gun技术)，Aebersold(ICAT技术)等科学家在蛋白质组学新方法的研究方面打开了一个崭新的局面。
目前，蛋白质组学面临的两大挑战是高丰度蛋白质压制低丰度蛋白质造成低丰度蛋白质检测困难以及蛋白质的定量问题。Shot-gun为代表的bottom-up技术在分离之前将蛋白质样品进行酶解，一个蛋白质酶解成多个肽段，这势必使原本就很复杂的样品变得更加复杂，不仅给色谱的分离能力与质谱的扫描速度提出挑战，不利于低丰度蛋白质的检测，而且将蛋白质酶解成肽段的同时又损失了完整蛋白质的信息。ICAT技术在蛋白质的相对定量方面发挥了重大作用，然而已有的定量技术仅局限在相对定量方面。因此，现有的多维色谱技术在解决蛋白质组学的两大问题上存在许多不足，本论文就是围绕当前蛋白质组学研究中存在的问题开展工作的，建立发展多维色谱技术方法达到实现高丰度蛋白质的去除以及完整蛋白质的分离鉴定以及定量等目的。
本论文共分五章。主要内容摘要如下：
第一章总结了蛋白质组学的现状与发展以及多维色谱与其相关技术在蛋白质组学中的应用与进展。介绍了二维／多维分离方法的理论依据，探讨了目前蛋白质组学研究使用的技术模式的成功与不足。并介绍了本论文选题的目的和意义，着重在于如何利用多维液相色谱的技术实现在完整蛋白水平上的分离，去除高丰度蛋白质以及利用多维液相色谱技术同时实现对蛋白质的定性定量等问题。
第二章以鼠肝为研究对象比较了不同的提取环境对动物组织中蛋白质提取的影响。主要研究了三种提取环境：酸性、中性和碱性环境。利用双向凝胶电泳分离成像技术比较了在三种不同环境下提取的蛋白质的分布的差异性，通过实验证明了在不同的提取环境下提取的蛋白质在种类和含量上都是不同的，同时也证明了在蛋白质组学的研究中不同的分离路线或分离模式应该根据具体分离条件的酸碱度的不同选用不同的蛋白提取方法，以避免在分离的过程中因沉淀问题而损失蛋白质，为后续工作打下基础。
第三章针对肝脏组织蛋白建立了反相高效液相色谱／双向凝胶电泳(RPLC／2-DE)的三维分离系统。2-DE技术是比较成熟的蛋白质分离手段，但是样品负载量低是影响中低丰度蛋白检测的一个重要原因，同时2-DE技术对于复杂的蛋白质样品的分离能力是有限的。RPLC是生物分析中常用的高效的分离模式，对蛋白或肽等有很好的分离能力，还具有除盐纯化样品的能力。RPLC与2-DE的分离机理正交，两种技术联合使用能在很大程度上提高样品的分辨率。本章工作以大鼠的肝脏组织蛋白为研究对象建立了实验路线并确立了实验条件。研究表明，蛋白质样品经过RPLC预分离之后，不同的蛋白就被富集浓缩到不同的馏份中，极大的提高了单个馏份中的蛋白在2-DE上的上样量和分辨率，这一点在凝胶扫描图上可以直观的反映出来，同时，实验证明RPLC分离蛋白质有着很好的重现性，据此可以对同一样品进行平行收集，以达到进一步增大单个馏份中蛋白的上样量的目的。因此，将RPLC作为预分离手段用于2-DE之前对样品进行预分离可以提高蛋白质在2-DE上的上样量和分辨率。这条技术路线已经在中国人肝项目表达谱的研究中得到应用。
第四章直接采用多维液相色谱的方法通过多维色谱分离的手段去除生物样品中的高丰度蛋白。中心思路就是：首先利用多维色谱技术对蛋白样品进行有效分离，在完整蛋白分离的基础上，将高丰度蛋白质在酶解成更复杂的肽段之前除掉。这条技术路线目前还没有类似报道。具体路线简述如下：
发展了强阳离子交换色谱／反相高效液相色谱(SCX／RPLC)分离系统，对鼠肝组织蛋白进行高效的分离。使用连续地线性盐梯度将蛋白质从SCX色谱柱上洗脱下来，得到62个馏份，每个馏份进一步使用常规的RPLC进行第二维地分离，整个分离过程使用紫外信号对蛋白的色谱峰进行监测，在第二维的分离过程中将信号强也就是量大的高丰度蛋白单独收集，其余中低丰度的蛋白进行合并、浓缩和酶解，然后使用毛细管反相色谱(cRPLC)进行分离，之后进行质谱鉴定，62个馏份分别如法炮制。结果表明，一次实验流程可以去除77个高丰度蛋白，占总蛋白量的34.5％，与不经过去除高丰度蛋白的样品进行比较，鉴定蛋白的数量提高了2到3倍之多。
在此基础上，我们进一步简化实验路线并提高方法地通量。来自SCX分离之后的62个馏份经过RPLC进一步分离之后，我们将所有含有中低丰度蛋白的洗脱液合并浓缩到一起，共同酶解之后使用在线的二维分离系统，即shot-gun技术对酶解之后的肽段进行分析鉴定。简化后的实验路线对中国人肝样品进行了分析，58个高丰度蛋白质被去除，共鉴定出1213个蛋白质。
总之，这套系统对降低蛋白质样品地复杂性，避免高丰度蛋白质在分离和质谱鉴定过程中压制中低丰度蛋白提供了一个新的手段和思路。另外，通过多维液相色谱分离的方法去除高丰度蛋白质，相对通常使用的免疫亲和的手段，无疑更具有通用性、灵活性、低成本和周期短的优势。
第五章发展了多维液相色谱的Top-down技术路线，即SCX／cRPLC／靶上酶解／MALDI-TOF-TOF分离鉴定系统。采用SCX／cRPLC分离系统，实现了在完整蛋白水平上的两维分离，本实验室发展的新方法靶上酶解技术的采用将蛋白质分离与质谱鉴定有效的结合起来，从而实现了蛋白从分离、酶解到鉴定这样一个完整的Top-down路线。蛋白质样品经过常规柱SCX分离之后，得到62个馏份，每个馏份继续使用毛细管反相柱cRPLC进行第二维分离，cRPLC作为第二维具有除盐和纯化样品的作用，为直接酶解提供了可能，利用自动点样仪将经过cRPLC的洗脱液直接收集到标准的MALDI靶板上，点样频率为30秒／个，经过靶上单点酶解之后用MALDI-TOF-TOF鉴定。整个系统对中国人肝蛋白进行了鉴定，共鉴定出3313个唯一蛋白。
与通常采用的shot-gun技术相比，我们发展的多维液相色谱的Top-down技术路线更能充分的分离蛋白质，得到更多的包括肽谱和疏水性等有关蛋白质的信息。与2-DE相比具有成本低和自动化高等优势。
在此基础上，我们进一步发展为三维蛋白分离系统，即SEC／SCX／RPLC系统，对肝脏蛋白进行更为完全的分离，利用紫外可见检测对蛋白峰进行归一化处理，进一步计算出蛋白的含量，相对应的蛋白质色谱峰同时进行浓缩、酶解、进而MALDI-TOF-TOF检测定性分析，以达到对单个蛋白同时进行定性和定量的目的。这条路线已经进行了有成效的探索，得到一些初步的结果，为蛋白质组学中的定量问题提供了一个可行的有价值的新思路。
总之，本论文围绕蛋白质组学的研究热点，以液相色谱分离系统为基础，发展了多种有效的分离系统，以完整蛋白质的分离为指导思想，建立了反相色谱预分离结合双向凝胶电泳的分离路线；开创了基于多维色谱分离为基础的高丰度蛋白质去除系统；发展了多维液相色谱的Top-down技术路线，试图在蛋白质研究主流的2-DE-MS技术之外，另辟蹊径，对蛋白组学新方法学的建立进行了有益的探索和研究，而且多数实验路线已经在中国人肝项目中投入使用，贡献了大量的有价值的实验数据。
Since 1950's, scientific interest has been increasingly shifting to molecular biology with the accomplishment of the gene sequencing of Human Genome Project (HGP). Proteomics has been the focus due to the role of executor of the life function. Proteomics refers to the analysis of all the proteins expressed in a cell or tissue. The investigation of functional proteome is of great significance given that functions of most of genes are still not well understood. Presently proteomic research focuses on differential proteome analysis of human diseases, which is designed to find key proteins with potentials to be used as markers for diagnosis or targets for medication. Proteomics is also becoming the spotlight of analytical chemistry.
2D PAGE is the most universal method for proteomics and posses high resolve power for proteins. Some problems in 2D PAGE, however, are still difficult to be overcome such as limited pH range, time-consuming and inefficient sensitivity for low abundant proteins. The reality has motivated considerable effort in developing new technique to resolve proteomics as alternative approach to 2D PAGE.
Liquid chromatography technologies are powerful technology to resolve proteins. But conventional one dimensional LC systems are incapable of completely resolving all the components in a complex mixture due to insufficient peak capacity. The development of two-or multi-dimensional column based separation techniques greatly improve the resolve power and peak capacity. During the past decade, a lot of analysts contributed to this field, such as Jorgenson's multi-dimensional separation, Yates' shot-gun technique, Aebersold's ICAT technique and so on.
This dissertation is divided into 6 parts.
In the first chapter, advances in 2D and multidimensional separation techniques were summarized with details. The theory basis of multidimensional separation techniques was introduced and the advantages and shortcomings of existing technical modes were discussed. The intention and meaning of this dissertation were explained.
In chapter 2, we used rat as animal model to compare the effect of different extraction conditions on the extracted proteins. The extract methods of tissue sample at acidic, neutral and basic pH were described and compared by using two-dimensional gel electrophoresis and reversed-phase liquid chromatography. The images on gel and mass spectra showed that the
different method can enrich proteins at different pH range. Different pH extract methods can be applied into corresponding liquid chromatography mode with the compatible mobile phase so that the loss and precipitation could be avoided. The good reproducibility enables the sample preparation methods to be widely applied in proteomics analysis.
In chapter 3, we describe an approach for fractionating complex protein samples from rat liver prior to 2-DE using RPLC. The study indicated that RPLC prefractionation can provide strong enrichment effect which enabled us to visualize additional and less abundance proteins. Chromatographic enrichment was also demonstrated by the peptide mass fingerprint data, which gave mass spectra with increased number of detected peptide and improved signal intensity. The reproducibility of this prefractionation technology allows pooling of several consecutive runs of the same sample, resulting in a highly enrichment of low abundance proteins. This technology route has been applied into the study of profiling mode of Chinese Human Liver Proteomics Project (CHLPP).
In chapter 4, for the first time a comprehensive two-dimensional (2D) liquid-phase separation system, coupling strong cation exchange chromatography (SCX) to reversed-phase high performance liquid chromatography (RPLC), instead of immuno-affinity chromatography, was developed at the intact protein level for depletion of high abundance proteins from rat liver. The core idea was to deplete the high abundance proteins before the digestion.
Proteins bound to the SCX phase were eluted off using a consecutive linear salt gradient. After salt fractionation, 62 fractions were obtained. Every fraction was separated further by RPLC. Ultraviolet signal was used to detect the separation process. The protein peaks with signal intensity above 0.1 AU was defined as high abundance proteins, whereas the other was defined as middle- or low high abundance protein. Then, the effluents contained high abundance proteins were collected individually and other effluents were pooled together. The combined middle- or low high abundance proteins were lyophilized, digested and separated by capillary reversed phase liquid chromatography (cRPLC). Mass spectrometry was used to analyze the protein. 62 fractions were treated using the same method. The results were that 77 high abundance proteins were depleted in an experimental process and identified proteins number was increased 2-3 times.
Based on the results, a simplified rapid-speed and high-throughput protocol was put forward further. Instead of separating every fraction using cRPLC, all effluents containing
middle- or low abundance protein were combined, enriched, digested and separated by online shotgun technology. The simplified method was used to analyze Chinese liver sample. 58 high abundance proteins were depleted and 1213 proteins were identified.
In summery, the system presented a novel idea about the depletion of high abundance proteins. In contrast with affinity technology, this strategy with the advantages of low-cost and saving-time has no bias to any proteins and could realize the global proteins analysis.
In chapter 5, for the first time, the 2-D separation platform based on the liquid chromatography combined with on-probe digestion technique and identification of mass spectrometry was constructed in intact proteins level for separation and identification of complex liver tissue proteins. The 2-D liquid chromatographic system was constructed by coupling SCX with cRPLC. Proteins were prefractionated by SCX according to charge in the first dimensional separation. 62 fractions eluting from the first dimension were subjected automatically to cRPLC to separate similarly charged proteins on the basis of their various hydrophobicities. A novel rapid on-target digestion technique was adopted to couple effectively the separation technique and mass spectrometry technique. After digestion, the matrix was deposited on the same spot, respectively. Then, the dried plate was analyzed by mass spectrometry. This new technology coupled the top-down approach and bottom-up technologies. The high efficiency of system was demonstrated for analysis of intact proteins from the soluble lysates of normal human liver. A total of 3313 proteins were identified.
We further developed three-dimensional separation system combined SEC with the SCX/RPLC mentioned above. This 3D system exhibited the potential of further high resolution for extremely complicated mixture. The intention of 3D system was to realize the identification and quantification of proteins. We had explored some relative experiments and made some effective results.
In a word, the main contributes of this dissertation is the development of effective separation system based multi-dimensional system. We aim at exploring and finding out new technological systems for proteomics, so that more breakthroughs can be obtained at the qualitative analysis and quantification study.
引文
[1] 王志珍，邹承鲁，后基因组—蛋白质组研究，生物化学与生物物理学报，1998，30(6)：533-699．
[2] 李淋，蛋白质组学的进展，生物化学与生物物理学报，2000，27(3)：227-231．
[3] M.R. Wi Iins, K.L. Williams, R.D. Appel, Proteome Research: NEW Frontiers in Functional Genomics. Springer-Vedag, 1997.
[4] 李伯良，李林，吴家睿，功能蛋白质组学，生物工程学报，2000，27(3)：227-231。
[5] Cordwell.S et al, Electrophoresis,1997,18:1393-1398.
[6] Wasinger V Cet al. Progress with gene-product of the Mollicutes: Mycoplasma genitalium, Elcectrophoresis, 1995, 16: 1090-1094.
[7] Wilin M R et al, From proteins to Proteomics: Large scale protein identification by two-dimensional electrophoresis and amide acid analysis, Bio Thchnology, 1996, 14: 61-65.
[8] 李伯良，功能蛋白质组学，生命的科学，1998，18(6)：1-4．
[9] 成海平，钱小红，蛋白质组研究的技术体系及其进展，生物化学与生物物理进展，2000，27(6)：584-588
[10] 于雁灵，复旦大学分析化学专业01级博士毕业论文．
[11] 贺福初，蛋白质组研究—后基因组时代的生力军，科学通报，1999，44(2)：113-122．
[12] 万晶红，贺福初，蛋白质组技术的研究进展，科学通报，1999，44(9)：904-911．
[13] 俞利荣，曾嵘，夏其昌，蛋白质组研究技术及其进展，生命的化学，1998，18(6)：10-16．
[14] 陈筱潇，药物蛋白质组学．药物研究的新思路，国外医学临床生物化学与检验学分册，2001，22(4)：212-214．
[15] 何大澄，肖雪媛，差异蛋白质组学及其应用，北京师范大学学报(自然科学版)，2002，38(4)：558-562．
[16] 郝鲁江，梁泉峰，生物信息学的发展及其应用，山东轻工业学院学报，2000，14(2)：37-41．
[17] 张迪，霍克克，顾科隆等，酵母双杂交技术研究进展，高技术通讯，2000，3：98-101
[18] 杨齐衡，李林，酵母双杂交技术及其在蛋白质组研究中的应用，生物化学与生物物理学报，1999，31(3)：221-225．
[19] 卞则梁，王光辉，质谱与生命科学，化学通报，1994，7：40-46．
[20] Johan Gobom, Martin Schuerenberg, Martin Mueller, Dorothea Theiss, et al, a-Cyano-4-hydroxycinnamic Acid Affinity Sample Preparation. A Protocol for MALDI-MS Peptide Analysis in Proteomics, Anal. Chem., 2001, 73: 434-438.
[21] James C. Hannis and David C. Muddiman, A Dual Electrospray Ionization Source Combined With Hexapole Accumulation to Achieve High Mass Accuracy of Biopolymers in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, J Am Soc Mass Spectrom, 2000,11, 876-883.
[22] Thomas P. Conrads, Gordon A. Anderson, Timothy D. Veenstra, Ljiljana Pas(?)a-Tolic', et al, Utility of Accurate Mass Tags for Proteome-Wide Protein Identification, Anal. Chem., 2000, 72: 3349-3354.
[23] Andrej Shevchenko, Matthias Wilm, Ole Vorm, and Matthias Mann, Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels, Anal. Chem., 1996, 68: 850-858.
[24] Andreas P. Jonsson, Youssef Aissouni, Carina Palmberg, Piergiorgio Percipalle, et al, Recovery of Gel-Separated Proteins for In-Solution Digestion and Mass Spectrometry, Anal. Chem., 2001, 73: 370-5377.
[25] K. Walhagen, K.K. Unger, M.T.W. Hearn, Capillary electroendoosmotic chromatography of peptides, Journal of Chromatography A, 2000, 887: 165-185.
[26] Michael P.Washburn, John R.Yates, New methods of proteome analysis: multidimensional chromatography and mass spectrometry, Proteomic: A trends guide, 2000: 27-30.
[27] Yun Jiang, Cheng S. Lee, On-line coupling of micro-enzyme reactor with micro-membrane chromatography for protein digestion, peptide separation, and protein identification using electrospray ionization mass spectrometry, Journal of Chromatography A, 2001, 924: 315-322.
[28] Jun Gao, Jingdong Xu, Laurie E. Locascio and Cheng S. Lee, Integrated Microfluidic System Enabling Protein Digestion, Peptide Separation, and Protein Identification, Anal. Chem., 2001, 73: 2648-2655.
[29] Michael T. Davis, Jill Beierle, Edward T. Bures, Michael D. McGinley, et al, Automated LC-LC-MS-MS platform using binary ion-exchange and gradient reversed-phase chromatography for improved proteomic analyses, Journal of Chromatography B, 2001, 752: 281-291.
[30] Shihong Wang, Fred E. Regnier, Proteolysis of whole cell extracts with immobilized enzyme columns as part of multidimensional chromatography, Journal of Chromatography A, 2001, 913: 429-436.
[31] Yufeng Shen, Rui Zhao, Mikhail E. Belov, Thomas P. Conrads, et al, Packed Capillary Reversed-Phase Liquid Chromatography with High-Performance Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Proteomics, Anal. Chem., 2001, 73: 1766-1775.
[32] Yufeng Shen, Nikola Tolic', Rui Zhao, Ljiljana Pas(?)a-Tolic', et al, High-Throughput Proteomics Using High-Efficiency Multiple-Capillary Liquid Chromatography with On-Line High-Performance ESI FTICR Mass Spectrometry, Anal. Chem., 2001, 73: 3011-3021.
[33] Andreas Premstaller, Herbert Oberacher, Wolfgang Walcher, et al., High-Performance Liquid Chromatography Electro-spray Ionization Mass Spectrometry Using Monolithic Capillary Columns for Proteomic Studies, Anal. Chem., 2001, 73: 2390-2396.
[34] Rachel R. Ogorzalek Loo, James D. Cavalcoli, Ruth A. VanBogelen, Charles Mitchell, et al, Virtual 2-D Gel Electrophoresis: Visualization and Analysis of the E. coliProteome by Mass Spectrometry, Anal. Chem., 2001, 73: 4063-4070.
[35] Steven Locke and Daniel Figeys, Techniques for the Optimization of proteomic Strategies Based on Head Column Stacking Capillary Electrophoresis, Anal. Chem., 2000, 72: 2684-2689.
[36] Pamela K. Jensen, Ljiljana Pas(?)a-Tolic', Gordon A. Anderson, Julie A. Horner, et al, Probing Proteomes Using Capillary Isoelectric Focusing-Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, 1999, 71: 2076-2084.
[37] Knut Wagner, Tasso Miliotis, Gyolrgy Marko-Varga, Rainer Bischoff, et al, An Automated On-Line Multidimensional HPLC System for Protein and Peptide Mapping with Integrated Sample Preparation, Anal. Chem., 2002, 74: 809-820.
[38] Hookeun Lee, Timothy J. Griffin, Steven P. Gygi, Beate Rist, et al, Development of a Multiplexed Microcapillary Liquid Chromatography System for High-Throughput Proteome Analysis, Anal. Chem., 2002, 74: 4353-4360.
[39] Zheru Zhang, Sergey Krylov, Edgar A. Arriaga, Robert Polakowski, et al, One-Dimensional Protein Analysis of an HT29 Human Colon Adenocarcinoma Cell, Anal. Chem., 2000, 72: 318-322.
[40] Tohru Natsume, Hiroshi Nakayama, Osten Jansson, Toshiaki Isobe, et al, Combination of Biomolecular Interaction Analysis and Mass Spectrometric Amino Acid Sequencing, Anal. Chem., 2000, 72: 4193-4198.
[41] Gerald Marie, Laurent Serani and Olivier Lapre′ vote, An On-Line Protein Digestion Device for Rapid Peptide Mapping by Electrospray Mass Spectrometry, Anal. Chem., 2000, 72: 5423-5430.
[42] Dirk A. Wolters, Michael P. Washburn and John R. Yates, An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics, Anal. Chem., 2001, 73: 5683-5690.
[43] Thierry Le Bihan, Devanon Pinto and Daniel Figeys, Nanoflow Gradient Generator Coupled with μ-LC-ESI-MS/MS for Protein Identification, Anal. Chem., 2001, 73: 1307-1315.
[44] 俞利荣，夏其昌等，人肝癌细胞系BEL-7404和正常肝细胞系L-02表达的蛋白质组双向凝胶电泳分析，科学通报，2000，45(2)：170-17．
[45] Li-rong Yu, Rong Zeng, Xiao-xia Shao, et al, Identification of differentially expressed proteins between human hepatoma and normal liver cell lines by two-dimensional electrophoresis and liquid chromatography-ion trap mass spectrometry, Electrophoresis, 2000, 21: 3058-3068.
[46] Youji Shimazaki, Seiichi Ohara, Takashi Manabe, Removal of specific protein spots on the patterns of non-denaturing two-dimensional electrophoresis using protein A agarose and antibodies, J. Biochem. Biophys. Methods, 1998, 37: 1-4.
[47] Haijun Sun, Yu-Ching E. Pan, Using native gel in two-dimensional PAGE for the detection of protein interactions in protein extract, J. Biochem. Biophys. Methods, 1999, 39: 143-151.
[48] Lan Huang, Min Shen, Igor Chernushevich, Alma L. Burlingame, et al, Identification and isolation of three proteasome subunits and their encoding genes from Trypanosoma brucei, Molecular and Biochemical Parasitology, 1999, 102: 211-223.
[49] Sarka Beranova-Giorgianni, Michael J. Pabst, Tara M. Russell, Francesco Giorgianni, et al, Preliminary analysis of the mouse cerebellum proteome, Molecular Brain Research, 2002, 98: 135-140.
[50] Yannicke Dauphin, Comparative studies of skeletal soluble matrices from some Scleractinian corals and Molluscs, International Journal of Biological Macromolecules, 2001, 28: 293-304.
[51] Anja Moller, Michael Soldan, Uwe Volker, Edmund Maser, Two-dimensional gel electrophoresis: a powerful method to elucidate cellular responses to toxic compounds, Toxicology, 2001,160:129-138.
[52] Seong Hwan Kim, Roman Vlkolinsky, Nigel Cairns, Michael Fountoulakis, et al, The reduction of NADH Ubiquinone oxidoreductase 24- and 75-kDa subunits in brains of patients with Down syndrome and Alzheimer's disease, Life Sciences, 2001, 68: 2741-2750.
[53] Peter W. Hewett, Identification of tumour-induced changes in endothelial cell surface protein expression: an in vitro model, The International Journal of Biochemistry & Cell Biology, 2001, 33: 325-335.
[54] Lirong Yu, Rong Zeng, Xiaoxia Shao, Nan Wang, et al, Identification of differentially expressed proteins between human hepatoma and normal liver cell lines by two-dimensional electrophoresis and liquid chromatography-ion trap mass spectrometry, Electrophoresis, 2000, 21: 2058-2068.
[55] Divis JM, Giddings JC, Statistical method for estimation of number of components from single complex chromatograms: theory, computer-based testing, and analysis of errors, Anal. Chem., 1985, 57: 2168-2177
[56] Giddings J C., Concepts and comparisons in multidimensional separation, J High Resolut. Chromatogr. Commun., 1987,10,319-323
[57] Liu Z., Patterson D.G., J r. Lee M L., Geometric approach to factor analysis for the estimation of orthogonality and practical peak capacity in comprehensive two-dimensional separation, Anal Chem , 1995 , 67(21) :3840-3845.
[58] Slonecker, P. J., Li X , Ridgway T H , Dorsey J G. Informational orthogonality of two-dimensional chromatographic separation, Anal Chem ,1996, 68 : 682-689.
[59] Murphy R E , Schure M R , Foley J P, Effect of sampling rate on resolution in comprehensive two-dimensional liquid chromatography, Anal Chem , 1998 , 70 :1585-1594.
[60] Issaq, H.J., Chan, K.C., Janini, G.M., Conrads, T.P., Veenstra, T.D. Multidimensional separation of peptides for effective proteomic analysis, J. Chromatogr. B, 2005, 817, 35-47.
[61] Bushey, M.M. , Jorgenson, J.W. , Automated instrumentation for comprehensive two-dimensional high-performance liquid chromatography of proteins, Anal.Chem., 1990, 62,161-167.
[62] Holland, L.A., Jorgenson, J.W., Separation of nanoliter samples of biological amines by a comprehensive two-dimensional microcolumn liquid chromatography system, Anal.Chem., 1995, 67, 3275-3283.
[63] Opiteck, GJ., Lewis, K.C., Jorgenson, J.W., Comprehensive on-line LC/LC/MS of proteins, Anal. Chem., 1997, 69,1518-1524.
[64] Opiteck, G.J.; Jorgenson, J.W. Two-dimensional SEC/RPLC coupled to mass spectrometry for the analysis of peptides, Anal.Chem., 1997, 69, 2283-2291.
[65] Wagner, K., Racaityte, K., Unger, K.K., Miliotis, T., Edhholm., L.E., Bischoff, R., Marko-varga,G., Protein mapping by two-dimensional high performance liquid chromatography, J. Chromatogr. A, 2000, 893, 293-305.
[66] Wagner, K.; Miliotis, T., Marko-varga, G., Bischoff, R., Unger, K.K. An automated on-linemultidimensional HPLC system for protein and peptide mapping with integrated sample preparation, Anal. Chem., 2002, 74, 809-820.
[67] Vissers, J.P.C., van Soest, R.E.J., Chervet, J-P., Cramers, C.A. Two-dimensional capillary liquid chromatography based on microfractionation, J. Microcolumn Sep., 1999, 11, 277-286.
[68] Wolters, D.A., Washburn, M.P., Yates III, J.R. An automated multidimensional protein identification technology for shotgun proteomics, Anal.Chem., 2001, 73, 5683-5690.
[69] Liu H., Lin D., Yates, JR III.,Multidimensional separations for protein/peptide analysis in the post-genomic era, Bio Technique, 2002, 32(4), 898-902.
[70] Zhang, Z., Smith, D.L., Smith, J.B. Multiple separations facilitate identification of protein variants by mass spectrometry, Proteomics, 2001, 1,1001-1009.
[71]Richter, R., Schulz Knappe, P., Schrader, M., Standker, L., Jurgens, M., Tammen, H., Forssmann, W.G. Composition of the peptide fraction in human blood plasma: database of circulating human peptides, J.Chromatopr.B, 1999,726, 25-35.
[72] Chen, Y., Wall, D., Lubman, D.M. Rapid identification and screening of proteins from whole cell lysates of human erythroleukemia cells in the liquid phase, using non-porous reversed phase high-performance liquid chromatography separations of proteins followed by multi-assisted laser desorption/ionization mass spectrometry analysis and sequence database searching, Rappid. Commun. Mass. Spectrom., 1998,12,1994-2003.
[73] Apffel, A., Chakel, J.A., Hancock, W.S., Souders, C, M'Timkulu, T., Pungor J.E. Application of multidimensional affinity high-performance liquid chromatography and electrospray ionization liquid chromatography-mass spectrometry to the characterization of glycosylation in single-chain plasminogen activator: Initial results, J.Chromatpgr.A, 1996,750, 35-42.
[74]Hsieh, Y. L. F., Wang, H.; Elicone, C., Mark, J., Martin, S. A., Regnier, F. Automated analytical system for the examination of protein primary structure, Anal. Chem., 1996, 68, 3, 455-462.
[75] Geng, M., Ji, J., Regnier, F.E. Signature-peptide approach to detecting proteins in complex mixtures, J. Chromatogr. A, 2000, 870, 295-313.
[76] Riggs, L.; Sioma, C.; Regnier, F.E. Automated signature peptide approach for proteomics, J. Chromatogr. A., 2001, 924, 359-368.
[77] Han, D.K. , Eng, J. , Zhou, H. , Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry, Nat. Biotechnol., 2001,19, 946-951.
[78]Goshe, M. B., Veenstra, T. D., Panisko, E. A., Conrads,T. P., Angell, N. H., Smith, R. D. Phosphoprotein isotope-coded affinity tags: Application to the enrichment and identification of low-abundance phosphoproteins, Anal. Chem., 2002, 74, 607-616.
[79] Ficarro, S.B., McCleland, M.L., Stukenberg, P.T., Burke, D.J., Ross, M.M., Shabanowitz, J.; Hunt, D.F.; White, F.M. Phosphoproteome analysis by mass sepectrometry and its application to saccharomyces cerevisiae, Nat. Biotechnol., 2002, 20, 301-305.
[80] Gygi, S. P., Rist, B., Griffin, T. J., Eng, J., Aebersold, R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags, J. Proteome Res., 2002,1, 47-54.
[81]Shen,Y., Jacobs, J.M., Camp II, D.G., Fang, R., Moore, R.J., Smith, R.D., Xiao,W., Davis, R.W. , Tompkins, R.G. Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome, Anal. Chem., 2004, 76,1134-1144.
[82] Jin, W.H., Dai, J, Li, S.J., Xia, Q.C., Zou, H.F., Zeng, R., Human Plasma Proteome Analysis by Multidimensional Chromatography Prefractionation and Linear Ion Trap Mass Spectrometry Identification, J. Proteome Res., 2005, 4, 613-619.
[83] Tu, C.J., Dai, J., Li, S.J., Sheng, Q.H., Deng, W.J., Qia, Q.C., Zeng, R., High-Sensitivity Analysis of Human Plasma Proteome by Immobilized Isoelectric Focusing Fractionation Coupled to Mass Spectrometry Identification, J. Proteome Res., 2005, 4,1265-1273.
[84] Li, R.X., Zhou, H., Li, S.J., Sheng, Q.H., Qia, Q.C., Zeng, R., Prefractionation of Proteome by Liquid Isoelectric Focusing Prior to Two-Dimensional Liquid Chromatography Mass Spectrometric Identification, J. Proteome Res., 2005, 4, 1256-1264.
[85] Wall, D. B., Kachman, M. T., Gong, S., Hinderer, R., Parus, S., Misek, D. E., Hanash, S. M., Lubman, D. M., Isoelectric Focusing Nonporous RP HPLC: A Two-Dimensional Liquid-Phase Separation Method for Mapping of Cellular Proteins with Identification Using MALDI-TOF Mass Spectrometry, Anal. Chem., 2000, 72,1099-1111.
[86] Kachman, M. T., Wang, H., Schwartz, D. R., Cho, K. R., Lubman, D. M. A 2-D Liquid Separations/Mass Mapping Method for Interlysate Comparison of Ovarian Cancers., Anal. Chem., 2002, 74,1779-1791.
[87] Zhu, K., Kim, J., Yoo, C, Miller, F. R., Lubman, D. M. High Sequence Coverage of Proteins Isolated from Liquid Separations of Breast Cancer Cells Using Capillary Electrophoresis-Time-of-Flight MS and MALDI-TOF MS Mapping, Anal. Chem., 2003, 75, 6209-6217.
[88] Yan, F., Subramanian, B., Nakeff, A., Barder, T. J., Parus, S. J., Lubman, D. M. A Comparison of Drug-Treated and Untreated HCT-116 Human Colon Adenocarcinoma Cells Using a 2-D Liquid Separation Mapping Method Based upon Chromatofocusing PI Fractionation, Anal. Chem., 2003, 75, 2299-2308.
[89] Zhu, Y., Lubman, D.M. Narrow-band fractionation of proteins from wholecell lysates using isoelectric membrane focusing and nonporous reversed-phase separations, Electrophoresis, 2004, 25, 949-958.
[90] Chen, J., Balgley, B. M., DeVoe, D. L., Lee, C. S. Capillary Isoelectric Focusing-Based Multidimensional Concentration/Separation Platform for Proteome Analysis, Anal. Chem., 2003, 75,3145-3152.
[91] Mohan, D., Pasˇa-Tolic', L., Masselon, C. D., Tolic', N., Bogdanov, B., Hixson, K. K., Smith, R. D., Lee, C. S. Integration of Electrokinetic-Based Multidimensional Separation/Concentration Platform with Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry for Proteome Analysis of Shewanella oneidensis, Anal. Chem., 2003, 75, 4432-4440.
[92] Wang, Y., Balgley, B.M., Rudnick, P.A., Evans, E.L., DeVoe, D.L., Lee, C.S. Integrated Capillary Isoelectric Focusing/Nano-reversed Phase Liquid Chromatography Coupled with ESI-MS for Characterization of Intact Yeast Proteins, J. Proteome Res., 2005, 4, 36-42.
[93] Meng, F., Cargile, B. J., Patrie, S. M., Johnson, J. R., McLoughlin, S. M., Kelleher, N. L. Processing Complex Mixtures of Intact Proteins for Direct Analysis by Mass Spectrometry, Anal. Chem., 2002, 74, 2923-2929.
[94] Meng, F., Du, Y., Miller, L. M., Patrie, S. M., Robinson, D. E., Kelleher, N. L. Molecular-Level Description of Proteins from Saccharomyces cerevisiae Using Quadrupole FT Hybrid Mass Spectrometry for Top Down Proteomics, Anal. Chem., 2004, 76, 2852-2858.
[1] Shaw MM, Riederer BM, Sample preparation for two-dimensional gel electrophoresis, Proteomics 2003, 3:1408-1417.
[2] Chertov O, Biragyn A, Kwak LW, Simpson JT, Boronina T, Hoang VM, Prieto DA, Conrads TP, Veenstra TD, Fisher RJ, Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry Proteomics, 2004, 4:1195-1203
[3] Tastet C, Charmont S, Chevallet M, Luche S, Rabilloud T, Structure-efficiency relationships of zwitterionic detergents as protein solubilizers in two-dimensional electrophoresis, Proteomics, 2003, 3:111-121.
[4] Luche S, Santoni V, Rabilloud T, Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis, Proteomics, 2003, 3:249-253.
[5] Henningsen R., Gale B.L., Straub K.M., DeNagel D.C., Application of zwitterionic detergents to the solubilization of integral membrane proteins for two-dimensional gel electrophoresis and mass spectrometry, Proteomics, 2002, 2(11): 1479-1488.
[6] Molloy M.P., Phadke N.D., Maddock J.R., Andrews P.C., Two-dimensional electrophoresis and peptide mass fingerprinting of bacterial outer membrane proteins, Electrophoresis, 2001, 22: 1686-1696.
[7] Molloy M.P., Herbert B.R., Slade M.B., Rabilloud T., Nouwens A.S., Williams K.L.,Gooley A.A., Proteomic analysis of the Escherichia coli outer membrane, Eur. J. Biochem., 2000, 267: 2871.
[8] Liberatori S., Bini L., De Felice C, Magi B., Marzocchi B., Raggiaschi R., Pallini V., Bracci R., Acute-phase proteins in perinatal human plasma, Electrophoresis, 1997,18: 520-526.
[9] O'Connell K.L., Stults J.T., Identification of mouse liver proteins on two-dimensional electrophoresis gels by matrix-assisted laser desorption ionization mass spectrometry of in situ enzymatic digests, Electrophoresis, 1997,18: 349-359.
[10] Sarto C, Marocchi A., Sanchez J-C, Giannone D., Frutiger S., Golaz O., Wilkins M.R., Doro G., Cappellano F., Hughes G., Hochstrasser D.F., Mocarelli P., Renal cell carcinoma and normal kidney protein expression, Electrophoresis, 1997,18: 599-604.
[11] Garfin DE, Two-dimensional gel electrophoresis: an overview, Trend in Analytical Chemistry, 2003, 22:263-272.
[12] Qu, Y., Moons, L., Vandesande, F., Determination of serotonin, catecholamins and their metabolites by direct injection of supernatants from chicken brain tissue homogenate using liquid chromatography with electrochemical detection . J. Chromatogr. B. 1997, 704, 351-358.
[13] Wei J, Sun J, Yu W, Jones A, Oeller P, Keller M, Woodnutt G, Short JM, Global proteome discovery using an online three-dimensional LC-MS/MS, J. Proteome Research, 2005, 4:801-808.
[14] Jin, W.H., Dai, J., Li, S. J., Xia, Q.C., Zou, H.F., Zeng, R., Human Plasma Proteome Analysis by Multidimensional Chromatography Prefractionation and Linear Ion Trap Mass Spectrometry Identification, J. Proteome Research, 2005, 4: 613-619.
[15] Tyan, Y. C, Wu, H.Y., Lai, W. W., Su, W. C, Liao, P. C, Proteomic Profiling of Human Pleural Effusion Using Two-Dimensional Nano Liquid Chromatography Tandem Mass, J. Proteome Research, 2005, 4:1274-1286.
[16] Ryden L, Carlsson J, in: Janson J, Ryden L (Eds.), High Resolution Methods, and Applications, VCH, Uppsala, 1989, pp. 252-274.
[17] Bae SH, Harris AG, Hains PG, Chen H, Garfin DE, Hazell SL, Paik YK, Walsh BJ, Cordwell SJ, Strategies for the enrichment and identification of basic proteins in proteome of projects, Proteomics, 2003, 3:569-579.
[18] Kline TR, Pang J, Hefta SA, Opiteck GJ, Kiefer SE, Scheffler JE, A high-yield method to extract peptides from rat brain tissue, Anal. Biochem., 2003, 315:183-188.
[1] Anderson, N. G., Matheson, A., Anderson, N. L. Back to the future: the human protein index (HPI) and the agenda for post-proteomic biology, Proteomics, 2001,1, 3-12.
[2] Hanash S. M., Biomedical applications of two-dimensional electrophoresis using immobilized pH gradients: Current status, Electrophoresis, 20002,1,1202-1209.
[3] Shevchenko, A., Wilm, M., Vorm, O., Mann, M., Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels, Anal. Chem. 1996, 68, 850-858.
[4] Anja Moller, Michael Soldan, Uwe Volker, Edmund Maser, Two-dimensional gelelectrophoresis: a powerful method to elucidate cellular responses to toxic compounds, Toxicology, 2001, 160: 129-138.
[5] Adamczyk, M., Gebler, J. C, Selective analysis of phosphopeptides within a proteinmixture by chemical modification, reversible biotinylation and mass spectrometry, J. Rapid Commun. Mass Spectrom 2001,15,1481-1488.
[6] Greenough, C.,Jenkins, R.E.,Kitteringham, N. R., Pirmohamed, M., Park, B. K., Pennington, S. R A method for the rapid depletion of albumin and immunoglobulin from human plasma, Proteomics 2004, 4, 3107-3111.
[7] R. Pieper, C.L. Gatlin, A.J. Makusky, P.S.,et al, Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome, Proteomics,2003, 3, 422-432.
[8] Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F, White F.M., Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae, Nat. Biotechnol., 2002, 20, 301-305.
[9] Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat. Biotechnol. 1999,17, 994-999.
[10] Badock, V., Steinhusen, U., Bommert, K., Otto, A., Prefractionation of protein samples for proteome analysis using reversed-phase high-performance liquid chromatography, Electrophoresis, 2001, 22, 2856-2864.
[11] Bergh, G. V., Clerens, S., Vandesande, F., Arckens, L., Reversed-phase high-performance liquid chromatography prefractionation prior to two-dimensional difference gel electrophoresis and mass spectrometry identifies new differentially expressed proteins between striate cortex of kitten and adult cat, Electrophoresis, 2003, 24,1471-1481.
[12] Butt, A., Davison, M. D., Smith, G. J., Young, J. A., Gaskell, S. J.,Oliver, S. G., Beynon, R. J., Chromatographic separations as a prelude to two-dimensional electrophoresis in proteomics analysis, Proteomics, 2001, 1, 42-53.
[13] Bier, M., Recycling isoelectric focusing and isotachophoresis, Electrophoresis 1998, 19, 1057-1063.
[14] Hannig, K., New aspects in preparative and analytical continuous free-flow cell electrophoresis, Electrophoresis 1982, 3, 235-243.
[15] Margolis J., Corthals G., Horvath Z.S., Preparative reflux electrophoresis, Electrophoresis 1995,16, 98-100.
[16] Horvath, Z. S., Gooley,A. A., Wrigley, C. W., Margolis, J., Williams, K.L. Preparative affinity membrane electrophoresis, Electrophoresis 1996,17, 224-226.
[17] P.G. Righetti, A. Castagna, B. Herbert, F. Reymond, J.S. Rossier, Prefractionation techniques in proteome analysis, Proteomics, 2003, 3, 1397-1407.
[18] H.R. Mahler, E.H.Cordes, Biological Chemistry, Harper &Row, New York 1971, pp. 441-461.
[19] Qu, Y., Moons, L., Vandesande, F. Determination of serotonin, catecholamins and their metabolites by direct injection of supernatants from chicken brain tissue homogenate using liquid chromatography with electrochemical detection . J. Chromatogr. B. 1997, 704, 351-358.
[20] G. Winkler, P. Wolschann, P. Briza, F.X. Heinz, C.J. Kunz, J. Chromatogr., 1985, 347: 83.
[21] Yeldandi A., Rao M., Reddy J., Mutation Research-fund Amental and Molecular Mechanisms of Muta Genesis, 2000,448:159-166.
[22] G. Kirby, C. Wolf, G. Neal, D. Judahdj, C. Henderson, P. Srivatanakulp, C. Wild, Carcinogenesis, 1993,14: 2613-2619.
[23] J. Yu, S. Yun, J. Lim, H. Kim, K. Kim, Proteome analysis of rat pancreatic acinar cells: Implication for cerulein-induced acute pancreatitis, Proteomics, 2003, 3: 2446-2453.
[24] G. Chen, T. Gharib, C. Huang, D. Thomas, K. Shedden, J. Taylor, S. Kardia, D. Misek, T. Giordano, M. Iannettoni, M. Orringer, S. Hanash, D. Beer, Proteomic analysis of lung adenocarcinoma: Identification of a highly expressed set of proteins in tumors, Clinical Cancer Research, 2002, 8: 2298-2305.
[25] I. Corbin, Y. Gong, M. Zhang, G. Minuk, Proliferative and nutritional dependent regulation of glyceraldehyde-3-phosphate dehydrogenase expression in the rat liver, Cell Proliferation, 2002, 35: 173-182.
[26] D. Goldenberg, S. Ayesh, T. Schneider, O. Pappo, O. Jurim, A. Eid, Y. Fellig, T. Dadon, I. Ariel, N. de Groot, A. Hochberg, E. Galun, Mol. Carcinogen, 2002 33,:113-117.
[1] Badock, V., Steinhusen, U.> Bommert, K., Otto, A.,Prefractionation of protein samples for proteome analysis using reversed-phase high-performance liquid chromatography, Electrophoresis 2001, 22, 2856-2864.
[2] Anderson, N. G., Matheson, A., Anderson, N. L. Back to the future: the human protein index (HPI) and the agenda for post-proteomic biology, Proteomics, 2001,1, 3-12
[3] Shevchenko, A.? Wilm, M.; Vorm, O., Mann, M. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels, Anal. Chem. 1996, 68, 850-858.
[4] Shaw, M. M., Riederer, B. M. Sample preparation for two-dimensional gel electrophoresis, Proteomics 2003, 3,1408-1417.
[5] Corthals, G. L., Wasinger, V. C.? Hochstrasser, D. F., Sanchez, J. C, The dynamic range of protein expression: A challenge for proteomic research, Electrophoresis, 2000, 21, 1104-1115.
[6] Wasinger, V. C., Pollack, J. D., Humphery, S. I.,The proteome of mycoplasma genitalium chaps-soluble component, Eur. J. Biochem. 2000, 267,1571-1582.
[7] Shen, Y. F., Jacobs, J. M., Camp, D. G., II, Fang, R. H., Moore, R. J., Smith, R. D., Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome.Anal. Chem. 2004, 76,1134-1144.
[8] Wu, C. C., MacCoss, M. J., Howell, K. E., Yates, J. R. III, A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 2003, 21, 532-538.
[9] McDonald, W. H., Ohi, R., Miyamoto, D. T., Mitchison, T. J., Yates, J. R. III, Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: single-dimension LC-MS/MS, 2-phase MudPIT, and 3-phase MudPIT, Int. J. Mass Spectrom. 2002,219, 245-251.
[10] Washburn, M. P., Wolters, D., Yates, J. R. III, Large-scale analysis of the yeast proteome by multidimensional protein identification technology .Nat. Biotechnol. 2001, 19, 242-247.
[11] Peng, J. M., Elias,J. E., Thoreen, C. C., Licklider, L. J., Gygi, S. P. Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. J. Proteome Res. 2003, 2, 43-50.
[12] Fujii, K., Nakano, T., Kawamura, T., Usui, F., Bando, Y., Wang, R., Nishimura, T. Multidimensional Protein Profiling Technology and Its Application to Human Plasma Proteome. J. Proteome Res. 2004, 3, 712-718.
[13] Dreger, M., Subcellular proteomics, Mass Spec Rev 2003, 22, 27-56
[14] N. Karoline Scheficer, Scott W. Millerc, Amy K. Carrollc, Christen Andersonc, et al, Two-dimensional electrophoresis and mass spectrometric identification of mitochondrial proteins from an SH-SY5Y neuroblastoma cell line, Mitochondrion, 2001,1: 161-179
[15] Bier, M., Recycling isoelectric focusing and isotachophoresis, Electrophoresis 1998, 19, 1057-1063.
[16] Hannig, K., New aspects in preparative and analytical continuous free-flow cell electrophoresis, Electrophoresis 1982, 3, 235-243.
[17] Margolis J., Corthals G., Horvath Z.S., Preparative reflux electrophoresis, Electrophoresis 1995,16, 98-100.
[18] Horvath, Z. S., Gooley, A. A., Wrigley, C. W., Margolis, J., Williams, K.L. Preparative affinity membrane electrophoresis, Electrophoresis 1996,17, 224-226.
[19] Van den Bergh G., Clerens, S., Vandesande, F., Arckens, L., Reversed-phase high-performance liquid chromatography prefractionation prior to two-dimensional difference gel electrophoresis and mass spectrometry identifies new differentially expressed proteins between striate cortex of kitten and adult cat, Electrophoresis, 2003, 24, 1471-1481.
[20] Butt, A., Davison, M. D., Smith, G. J., Young, J. A., Gaskell, S. J.,Oliver, S. G., Beynon, R. J., Chromatographic separations as a prelude to two-dimensional electrophoresis in proteomics analysis, Proteomics, 2001,1, 42-53.
[21] Jacobs, J. M., Mottaz, H. M., Yu, L. R., Anderson, D. J., Moore, R. J., Chen, W.N. U., Auberry, K. J., Strittmatter, E. F., Monroe, M. E., hrall, B. D., Camp, D. G. II, Smith, R. D. J. Proteome Res. 2004, 3, 68-75.
[22] Adamczyk, M., Gebler, J. C.Wu, Selective analysis of phosphopeptides within a protein mixture by chemical modification, reversible biotinylation and mass spectrometry, J. Rapid Commun. Mass Spectrom 2001,15,1481-1488.
[23] Greenough, C, Jenkins, R.E., Kitteringham, N. R., Pirmohamed, M., Park, B. K., Pennington, S. R A method for the rapid depletion of albumin and immunoglobulin from human plasma, Proteomics 2004, 4, 3107-3111.
[24] Pieper R., Gatlin C.L., Makusky A.J., et al, Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome, Proteomics,2003, 3, 422-432.
[25] Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F, White F.M., Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae, Nat. Biotechnol., 2002, 20, 301-305.
[26] Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat. Biotechnol. 1999,17, 994-999.
[27] Qu, Y., Moons, L., Vandesande, F. Determination of serotonin, catecholamins and their metabolites by direct injection of supernatants from chicken brain tissue homogenate using liquid chromatography with electrochemical detection . J. Chromatogr. B. 1997, 704, 351-358.
[28] Zhang, X. M., Huang, S. Single step on-column frit making for capillary high-performance liquid chromatography using sol-gel technology J. Chromatogr. A 2001, 910,13-18.
[29] Mao, Y., Zhang, X. M. Comprehensive two-dimensional separation system by coupling capillary reverse-phase liquid chromatography to capillary isoelectric focusing for peptide and protein mapping with laser-induced fluorescence detection Electrophoresis 2003, 24, 3289-3295.
[30] Yang, X. H., Zhang, X. M., Li, A. Z., Zhu, S. Y., Huang, Y. P. Comprehensive two-dimensional separations based on capillary high-performance liquid chromatography and microchip electrophoresis.Electrophoresis 2003, 24,1451-1457.
[31] Zhang, J., Hu, H. L., Gao, M. X., Yang, P. Y., Zhang, X. M. Comprehensive two-dimensional chromatography and capillary electrophoresis coupled with tandem time-of-flight mass spectrometry for high-speed proteome analysis.Electrophoresis 2004, 25, 2374-2383.
[32] Wang, Y., Zhang, J., Liu, C. L., Gu, X., Zhang, X. M. Nano-flow multidimensional liquid chromatography with electrospray ionization time-of-flight mass spectrometry for proteome analysis of hepatocellular carcinoma Analytica Chimica Acta, 2005, 530, 227-235.
[33] Bordin, G., Cordeiro Raposo, F., Calle, B. de la, Rodriguez, A.R. Identification and quantification of major bovine milk proteins by liquid chromatography. J. Chromatogr. A, 2001, 928, 63-76.
[34] Ferreira, I.M.P.L.V.O., Cacote, H. Detection and quantification of bovine, ovine and caprine milk percentages in protected denomination of origin cheeses by reversed-phase high-performance liquid chromatography of beta-lactoglobulins.J. Chromatogr. A, 2003, 1015,111-118.
[35] Merbel, N. C. van de, Mentink, C. J.A.L., Hendriks, G.,Wolffenbuttel, B.H.R. Liquid chromatographic method for the quantitative determination of iV-carboxymethyllysine in human plasma proteins. J. Chromatogr. B, 2004, 808,163-168.
[36] Bu¨nger, H., Kaufner, L., Pison, U. Quantitative analysis of hydrophobic pulmonary surfactant proteins by high-performance liquid chromatography with light-scattering detection J. Chromatogr. A, 2000, 870 363-369.
[37] Toorop, R.M., Murch, S.J., Ball, R.O., Development of a rapid and accurate method for separation and quantification of myofibrillar proteins in meat, Food Res. International, 1997, 30, 619-627.
[38] Zhu, H.N., Pan, S.Q., Gu, S., Bradbury, E.M. ,Chen, X. Amino acid residue specific stable isotope labeling for quantitative proteomics., Rapid Commun. Mass Spectrom, 2002,16, 2115-2123.
[39] Gu, S., Du, Y.C., Chen, J., Liu, Z.H., Bradbury, E.M., Hu, C.A., Chen, X. Large-Scale Quantitative Proteomic Study of PUMA-Induced Apoptosis Using Two-Dimensional Liquid Chromatography-Mass Spectrometry Coupled with Amino Acid-Coded Mass Tagging, J. Proteome Res. 2004, 3,1191-1200.
[40] Gu, S., Liu, Z.H., Pan, S.Q., Jiang, Z.Y., Lu, H.M., Bradbury, E.M., Hu, C.A., Chen, X. Global Investigation of p53-induced Apoptosis Through Quantitative Proteomic Profiling Using Comparative Amino Acid-coded Tagging; Molecular & Cellular Proteomics, 2004, 3, 998-1008.
[41] Gao, M.X., Jin, H., Yang, P.Y., Zhang, X.M. Chromatographic prefractionation prior to two-dimensional electrophoresis and mass spectrometry identifies: Application to the complex proteome analysis in rat liver, Analytica Chimica Acta, 2005, 553, 83-92.
[42] Hochstrasser, D. E, Wilkins, M. R., Williams, K. L., Appel,R. D., Hochstrasser, D. E (Eds.), Proteome Research: New Frontiers in Functional Genomics, Springer, New York 1997,pp. 187.
[43] Tang, Z.Y., Sun, F.X., Tian, J., Ye, S.L, Liu, Y.K., Liu, K.D., Xue, Q., Chen, J., Xia, J.L., Qin, L.X., Sun, H.C., et al, World J Gastroenterol 2001, Oct 7(5):597-603.
[44] Sun, F.X., Tang, Z.Y., Liu, K.D., Ye, S.L., Xue, Q., Zhonghua Yixue Zazhi, 1995,75:673-685.
[45] Sun, F. X., Tang, Z,Y., Liu, K.D., Ye, S.L., Xue, Q., Gao, D,M,, Ma, Z.C., Int J Cancer, 1996,66:239-245
[46] 汤钊猷，肝癌转移复发的基础与临床，上海科技教育出版社，2003．
[47] Sam Hanash, Building a foundation for the human proteome organization,J. Proteome Res., 2004, 3, 197-199.
[48] Lescuyer, P., Hochstrasser, D.F., Sanchez, J.C., Comprehensive proteome analysis by chromatographic protein prefractionation, Electrophoresis, 2004, 25, 1125-1135.
[1] Venter J C, Adams M D, Myers E W, Li P W, Mural R J, Sutton G G, Smith H O, Yandell M, Evans C A, Holt R A, et al .The sequence of human genome, Science, 2001,291 : 1304-1351.
[2] Lander E S, Linton L M, Birren B, Nusbaum C, Zody M C ,Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, FunkeR, Gage D, et al, Initial sequencing and analysis of the human genome, Nature, 2001,409 : 860-921.
[3] Naaby-Hansen S, Waterfield M D, Cramer R., Proteomics-post-genomic cartography to understand gene function, Trends in Pharmacological Sciences, 2001,22 (7) : 376-384.
[4] 贺福初，蛋白质组研究—后基因组时代的生力军，科学通报，1999，44(2)：113-122．
[5] 张养军，蔡耘，王京兰，李晓海，钱小红，蛋白质组学研究中的色谱分离技术，色谱，2003，21，120-26．
[6] Chen H, Horvath C, High-speed high-performance liquid chromatography of peptides and proteins, J chromatography A, 1995, 705: 3-20.
[7] Dolnik V, Hutterer KM, Capillary electrophoresis of proteins 1999-2001, Electrophoresis, 2001, 22: 4163-4178.
[8] Giddings JC, Concepts and comparisons in multidimensional separation, J High Resoluti. Chromatogr. Commun., 1987, 10: 319-323.
[9] Divis JM, Giddings JC, Statistical method for estimation of number of components from single complex chromatograms: theory, computer-based testing, and analysis of errors, Anal. Chem. 1985, 57: 2168-2177.
[10] Divis JM, Giddings JC, Statistical method for estimation of number of components from single complex chromatograms: application to experimental chromatograms, Anal. Chem. 1985, 2178-2185.
[11] Jinzhi Chen, Cheng S. Lee, Yufeng Shen, Richard D. Smith, Eric H Baehrecke, Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation, electrophoresis, 2002, 23: 3143-3148.
[12] Hongbin Liu, Dayin Lin, John R. Yate Ⅲ, Multidimensional separations for protein/peptide analysis in the post-genomic era, Biotechniques, 2002, 32, 4: 898-911.
[13] 张丽华，张维冰，张玉奎，马场嘉信，多维高效液相色谱／毛细管电泳模式在蛋白质研究中的应用，色谱，2003，21，1：32-37．
[14] Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., Yates, J. R. Ⅲ, Direct analysis of protein complexes using mass spectrometry Nat. Biotechnol.,1999, 17, 676-682.
[15] Wu, C. C., MacCoss, M. J., Howell, K. E., Yates, J. R. Ⅲ,A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol., 2003, 21, 532-538.
[16] Washburn, M. P., Wolters, D., Yates, J. R. Ⅲ, Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol., 2001,19, 242-247.
[17] Shen, Y., Jacobs, J. M., Camp, D. G., Ⅱ, Fang, R., Moore, R. J., Smith, R. D., Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal. Chem., 2004, 76, 1134-1144.
[18] Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., Gygi, S. P., Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. J. Proteome Res., 2003, 2, 43-50.
[19] Fujii, K., Nakano, T., Kawamura, T., Usui, F., Bando, Y., Wang, R., Nishimura, T., Multidimensional Protein PrOfiling Technology and Its Application to Human Plasma Proteome. J. Proteome Res., 2004, 3, 712-718.
[20] Han, D. K., Eng, J., Zhou, H., Aebersold, R., Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol., 2001, 19, 946-951.
[21] VerBerkmoes, N. C., Bundy, J. L., Hauser, L., Asano, K. G., Razumovskaya, J., Larimer, F., Hettich, R. L., Stephenson, J. L. Jr., Integrating "Top-Down" and "Bottom-Up" Mass Spectrometric Approaches for Proteomic Analysis of Shewanella oneidensis. J. Proteome Res., 2002, 1,239-252.
[22] Gygi, S. P., Rist, B., Griffin, T. J., Eng, J., Aebersold, R., Proteome Analysis of Low-Abundance Proteins Using Multidimensional Chromatography and Isotope-Coded Affinity Tags. J. Proteome Res., 2002,1, 47-54.
[23] Wu, S.-L., Choudhary, G., Ramstrom, M., Bergquist, J., Hancock, W. S. Evaluation of Shotgun Sequencing for Proteomic Analysis of Human Plasma Using HPLC Coupled with Either Ion Trap or Fourier Transform Mass Spectrometry J. Proteome Res., 2003, 2, 383-393.
[24] Mann, M., Jensen, O. N., Proteomic analysis of post-translational modifications. Nat. Biotechnol., 2003, 2, 255-261.
[25] MacCoss, M. J., McDonald, W. H., Saraf, A., Sadygov, R., Clark, J. M., Tasto, J. J., Gould, K. L., Wolters, D., Washburn, M., Weiss, A., Clark, J. I., Yates, J. R. III, Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci., U.S.A., 2002, 99, 7900-7905.
[26] Choudhary, G., Wu, S.L., Shieh, P., Hancock, W. S., Multiple Enzymatic Digestion forEnhanced Sequence Coverage of Proteins in Complex Proteomic Mixtures Using Capillary LC with Ion Trap MS/MS. J. Proteome Res., 2003, 2, 59-67.
[27] Wall, D. B., Kachman, M. T., Gong, S., Hinderer, R., Parus, S., Misek, D. E., Hanash, S. M., Lubman, D. M., Isoelectric Focusing Nonporous RP HPLC: A Two-Dimensional Liquid-Phase Separation Method for Mapping of Cellular Proteins with Identification Using MALDI-TOF Mass Spectrometry, Anal. Chem., 2000, 72,1099-1111.
[28] Kachman, M. T., Wang, H., Schwartz, D. R., Cho, K. R., Lubman, D. M., A 2-D Liquid Separations/Mass Mapping Method for Interlysate Comparison of Ovarian Cancers, Anal. Chem., 2002, 74,1779-1791.
[29] Zhu, K., Kim, J., Yoo, C, Miller, F. R., Lubman, D. M., High Sequence Coverage of Proteins Isolated from Liquid Separations of Breast Cancer Cells Using Capillary Electrophoresis-Time-of-Flight MS and MALDI-TOF MS Mapping, Anal. Chem., 2003, 75, 6209-6217.
[30] Yan, F., Subramanian, B., Nakeff, A., Barder, T. J., Parus, S. J., Lubman, D. M., A Comparison of Drug-Treated and Untreated HCT-116 Human Colon Adenocarcinoma Cells Using a 2-D Liquid Separation Mapping Method Based upon Chromatofocusing PI Fractionation, Anal. Chem., 2003, 75, 2299-2308.
[31] Zhu, Y., Lubman, D.M., Narrow-band fractionation of proteins from wholecell lysates using isoelectric membrane focusing and nonporous reversed-phase separations Electrophoresis, 2004, 25, 949-958.
[32] Chen, J., Balgley, B. M., DeVoe, D. L., Lee, C. S., Capillary Isoelectric Focusing-Based Multidimensional Concentration/Separation Platform for Proteome Analysis, Anal. Chem., 2003, 75, 3145-3152.
[33] Mohan, D., PasVTolic', L., Masselon, C. D., Tolic', N., Bogdanov, B., Hixson, K. K., Smith, R. D., Lee, C. S., Integration of Electrokinetic-Based Multidimensional Separation/Concentration Platform with Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry for Proteome Analysis of Shewanella oneidensis, Anal. Chem., 2003, 75, 4432-4440.
[34] Wang, Y., Balgley, B.M., Rudnick, P.A., Evans, E.L., DeVoe, D.L., Lee, C.S., Integrated Capillary Isoelectric Focusing/Nano-reversed Phase Liquid Chromatography Coupled with ESI-MS for Characterization of Intact Yeast Proteins, J. Proteome Res., 2005, 4, 36-42.
[35] Meng, F., Cargile, B. J., Patrie, S. M., Johnson, J. R., McLoughlin, S. M., Kelleher, N. L., Processing Complex Mixtures of Intact Proteins for Direct Analysis by MassSpectrometry, 2002, Anal. Chem., 74, 2923-2929.
[36] Meng, F., Du, Y., Miller, L. M., Patrie, S. M., Robinson, D. E., Kelleher, N. L.,Molecular-Level Description of Proteins from Saccharomyces cerevisiae Using Quadrupole FT Hybrid Mass Spectrometry for Top Down Proteomics, Anal. Chem., 2004,76, 2852-2858.
[37] Dogruel, D., Williams, P., Nelson, R.W., Rapid Tryptic Mapping Using Enzymically Active Mass Spectrometer Probe Tips, Anal. Chem., 1995, 67,4343-4348.
[38] Hsieh, Y.L.F., Wang, H.Q., Elicone, C, Mark, J., Martin, S.A., Regnier, F., Automated Analytical System for the Examination of Protein Primary Structure, Anal. Chem., 1996, 68, 455-462.
[39] Sakai-Kato, K., Kato, M., Toyo'oka, T., On-Line Trypsin-Encapsulated Enzyme Reactor by the Sol-Gel Method Integrated into Capillary Electrophoresis, Anal. Chem., 2002, 74, 2943-2949.
[40] Cooper, J.W., Chen, J., Li, Y., Lee, C.S., Membrane-Based Nanoscale Proteolytic Reactor Enabling Protein Digestion, Peptide Separation, and Protein Identification Using Mass Spectrometry, Anal. Chem., 2003, 75,1067-1074.
[41] Samskog, J., Bylund, D., Jacobsson, S.P., Markides, K.E., Miniaturized on-line proteolysis-capillary liquid chromatography-mass spectrometry for peptide mapping of lactate dehydrogenase, J. Chromatogr. A., 2003, 998, 83-91.
[42] Ericsson, D., Ekstro¨m, S., Nilsson, J., Bergquist, J., Marko-Varga, G., Laurell, T., Downsizing proteolytic digestion and analysis using dispenser-aided sample handling and nanovial matrix-assisted laser/desorption ionization-target arrays, Proteomics, 2001, 1, 1072-1081.
[43] Slysz, G.W., Schriemer, D.C., On-column digestion of proteins in aqueous-organic solvents, Rapid Commun. Mass Spectrom., 2003, 17, 1044-1050.
[44] Slysz, G.W., Schrieme, D.C., Blending Protein Separation and Peptide Analysis through Real-Time Proteolytic Digestion, Anal. Chem., 2005, 77,1572-1579.
[45] Harris, W.A., Reilly, J.P., On-probe digestion of Bacterial proteins for MALDI-MS, Anal. Chem., 2002, 74, 4410-4416.
[46] Gobom, J., Nordhoff, E., Ekman, R., Roepstorff, P., Rapid micro-scale proteolysis of proteins for MALDI-MS peptide mapping using immobilized trypsin, Int. J. Mass Spectrom. Ion Processes., 1997,169,153-163.
[47] Kussmann, M., Nordhoff, E., Rahbek-Nielsen, H., Haebel, S., Rossel-Larsen, M., Jakobsen, L., Gobom, J., Mirgorodskaya, E., Kroll-Kristensen, A., Palm, L., Roepstorff, P., Matrix-assisted Laser Desorption/ Ionization Mass Spectrometry Sample Preparation Techniques Designed for Various peptide and protein analystes, J. Mass Spectrom., 1997, 32, 593-601.
[48] Dai, Y., Whittal, R. M., Li, L., Two-Layer Sample Preparation: A Method for MALDI-MS Analysis of Complex Peptide and Protein Mixtures, Anal. Chem., 1999,71,1087-1091.
[49] Ericson, C, Phung, Q. T., Horn, D. M., Peters, E. C, Fitchett, J. R., Ficarro, S. B., Salomon, A. R., Brill, L. M., Brock, A., An Automated Noncontact Deposition Interface for Liquid Chromatography Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry, Anal. Chem., 2003, 75,2309-2315.
[50] Mao, Y., Zhang, X., Comprehensive two-dimensional separation system by coupling capillary reverse-phase liquid chromatography to capillary isoelectric focusing for peptide and protein mapping with laser-induced fluorescence detection Electrophoresis, 2003, 24, 3289-3295.
[51] Yang, X., Zhang, X., Li, A., Zhu, S., Huang, Y., Comprehensive two-dimensional separations based on capillary high-performance liquid chromatography and microchip electrophoresis. Electrophoresis, 2003, 24,1451-1457.
[52] Zhang, J., Hu, H., Gao, M., Yang, P., Zhang, X., Comprehensive two-dimensional chromatography and capillary electrophoresis coupled with tandem time-of-flight mass spectrometry for high-speed proteome analysis. Electrophoresis, 2004, 25, 2374-2383
[53] Wang, Y., Zhang, J., Liu, C. L., Gu, X., Zhang, X. M., Nano-flow multidimensional liquid chromatography with electrospray ionization time-of-flight mass spectrometry for proteome analysis of hepatocellular carcinoma, Analytica Chimica Acta, 2005, 530, 227-235.
[54] Qu, Y.; Moons, L.; Vandesande, F. Determination of serotonin, catecholamins and their metabolites by direct injection of supernatants from chicken brain tissue homogenate using liquid chromatography with electrochemical detection. J. Chromatogr. B. 1997, 704, 351-358.
[55] Zhang, X., Huang, S., Single step on-column frit making for capillary high-performance liquid chromatography using sol-gel technology J. Chromatogr. A., 2001, 910,13-18
[56] Zuo, X., Echan, L., Hembach, P., Tang, H. Y., Speicher, K. D., Santoli, D., Speicher, D. W., Towards global analysis of mammalian proteomes using sample prefractionation prior to narrow pH range two-dimensional gels and using onedimensional gels for insoluble and large proteins Electrophoresi, 2001, 22,1603-1615.
[57] Zuo, X., Speicher, D. W., Comprehensive analysis of complex proteomes using microscale solution isoelectrofocusing prior to narrow pH range two-dimensional electrophoresis Proteomics, 2002, 2, 58-68.
[58] Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol., 1999,17, 994-999.
[59] Zhu, H., Pan, S., Gu, S., Bradbury, E.M., Chen, X., Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom., 2002,16, 2115-2123.
[60] Gu, S., Du, Y., Chen, J., Liu, Z., Bradbury, E.M., Hu, C.A., Chen, X., Large-Scale Quantitative Proteomic Study of PUMA-Induced Apoptosis Using Two-Dimensional Liquid Chromatography-Mass Spectrometry Coupled with Amino Acid-Coded Mass Tagging. J. Proteome Res., 2004, 3, 1191-1200.
[61] Gu, S., Liu, Z., Pan, S., Jiang, Z., Lu, H., Bradbury, E.M., Hu, C.A., Chen, X., Global Investigation of p53-induced Apoptosis Through Quantitative Proteomic Profiling Using Comparative Amino Acid-coded Tagging. Molecular & Cellular Proteomics, 2004, 3, 998-1008.
[62] Bordin, G., Raposo, F. C, Calle, B. de la, Rodriguez, A.R., Identification and quantification of major bovine milk proteins by liquid chromatography. J. Chromatogr. A, 2001, 928, 63-76.
[63] Ferreira, I.M.P.L.V.O., Cacote, H., Detection and quantification of bovine, ovine andcaprine milk percentages in protected denomination of origin cheeses by reversed-phase high-performance liquid chromatography of beta-lactoglobulins. J. Chromatogr. A., 2003, 1015,111-118.
[64] Merbel, N. C. van de, Mentink, C. J.A.L., Hendriks, G., Wolffenbuttel, B.H.R. Liquid chromatographic method for the quantitative determination of N-carboxymethyllysine in human plasma proteins. J. Chromatogr. B, 2004, 808,163-168.
[65] Bu¨nger, H.; Kaufner, L.; Pison, U., Quantitative analysis of hydrophobic pulmonary surfactant proteins by high-performance liquid chromatography with light-scattering detection. J. Chromatogr. A, 2000, 870, 363-369.
[66] Toorop, R.M., Murch, S.J., Ball, R.O., Development of a rapid and accurate method for separation and quantification of myofibrillar proteins in meat. Food Res. International, 1997, 30, 619-627.
[2] 李淋，蛋白质组学的进展，生物化学与生物物理学报，2000，27(3)：227-231．
[3] M.R. Wi Iins, K.L. Williams, R.D. Appel, Proteome Research: NEW Frontiers in Functional Genomics. Springer-Vedag, 1997.
[4] 李伯良，李林，吴家睿，功能蛋白质组学，生物工程学报，2000，27(3)：227-231。
[5] Cordwell.S et al, Electrophoresis,1997,18:1393-1398.
[6] Wasinger V Cet al. Progress with gene-product of the Mollicutes: Mycoplasma genitalium, Elcectrophoresis, 1995, 16: 1090-1094.
[7] Wilin M R et al, From proteins to Proteomics: Large scale protein identification by two-dimensional electrophoresis and amide acid analysis, Bio Thchnology, 1996, 14: 61-65.
[8] 李伯良，功能蛋白质组学，生命的科学，1998，18(6)：1-4．
[9] 成海平，钱小红，蛋白质组研究的技术体系及其进展，生物化学与生物物理进展，2000，27(6)：584-588
[10] 于雁灵，复旦大学分析化学专业01级博士毕业论文．
[11] 贺福初，蛋白质组研究—后基因组时代的生力军，科学通报，1999，44(2)：113-122．
[12] 万晶红，贺福初，蛋白质组技术的研究进展，科学通报，1999，44(9)：904-911．
[13] 俞利荣，曾嵘，夏其昌，蛋白质组研究技术及其进展，生命的化学，1998，18(6)：10-16．
[14] 陈筱潇，药物蛋白质组学．药物研究的新思路，国外医学临床生物化学与检验学分册，2001，22(4)：212-214．
[15] 何大澄，肖雪媛，差异蛋白质组学及其应用，北京师范大学学报(自然科学版)，2002，38(4)：558-562．
[16] 郝鲁江，梁泉峰，生物信息学的发展及其应用，山东轻工业学院学报，2000，14(2)：37-41．
[17] 张迪，霍克克，顾科隆等，酵母双杂交技术研究进展，高技术通讯，2000，3：98-101
[18] 杨齐衡，李林，酵母双杂交技术及其在蛋白质组研究中的应用，生物化学与生物物理学报，1999，31(3)：221-225．
[19] 卞则梁，王光辉，质谱与生命科学，化学通报，1994，7：40-46．
[20] Johan Gobom, Martin Schuerenberg, Martin Mueller, Dorothea Theiss, et al, a-Cyano-4-hydroxycinnamic Acid Affinity Sample Preparation. A Protocol for MALDI-MS Peptide Analysis in Proteomics, Anal. Chem., 2001, 73: 434-438.
[21] James C. Hannis and David C. Muddiman, A Dual Electrospray Ionization Source Combined With Hexapole Accumulation to Achieve High Mass Accuracy of Biopolymers in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, J Am Soc Mass Spectrom, 2000,11, 876-883.
[22] Thomas P. Conrads, Gordon A. Anderson, Timothy D. Veenstra, Ljiljana Pas(?)a-Tolic', et al, Utility of Accurate Mass Tags for Proteome-Wide Protein Identification, Anal. Chem., 2000, 72: 3349-3354.
[23] Andrej Shevchenko, Matthias Wilm, Ole Vorm, and Matthias Mann, Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels, Anal. Chem., 1996, 68: 850-858.
[24] Andreas P. Jonsson, Youssef Aissouni, Carina Palmberg, Piergiorgio Percipalle, et al, Recovery of Gel-Separated Proteins for In-Solution Digestion and Mass Spectrometry, Anal. Chem., 2001, 73: 370-5377.
[25] K. Walhagen, K.K. Unger, M.T.W. Hearn, Capillary electroendoosmotic chromatography of peptides, Journal of Chromatography A, 2000, 887: 165-185.
[26] Michael P.Washburn, John R.Yates, New methods of proteome analysis: multidimensional chromatography and mass spectrometry, Proteomic: A trends guide, 2000: 27-30.
[27] Yun Jiang, Cheng S. Lee, On-line coupling of micro-enzyme reactor with micro-membrane chromatography for protein digestion, peptide separation, and protein identification using electrospray ionization mass spectrometry, Journal of Chromatography A, 2001, 924: 315-322.
[28] Jun Gao, Jingdong Xu, Laurie E. Locascio and Cheng S. Lee, Integrated Microfluidic System Enabling Protein Digestion, Peptide Separation, and Protein Identification, Anal. Chem., 2001, 73: 2648-2655.
[29] Michael T. Davis, Jill Beierle, Edward T. Bures, Michael D. McGinley, et al, Automated LC-LC-MS-MS platform using binary ion-exchange and gradient reversed-phase chromatography for improved proteomic analyses, Journal of Chromatography B, 2001, 752: 281-291.
[30] Shihong Wang, Fred E. Regnier, Proteolysis of whole cell extracts with immobilized enzyme columns as part of multidimensional chromatography, Journal of Chromatography A, 2001, 913: 429-436.
[31] Yufeng Shen, Rui Zhao, Mikhail E. Belov, Thomas P. Conrads, et al, Packed Capillary Reversed-Phase Liquid Chromatography with High-Performance Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Proteomics, Anal. Chem., 2001, 73: 1766-1775.
[32] Yufeng Shen, Nikola Tolic', Rui Zhao, Ljiljana Pas(?)a-Tolic', et al, High-Throughput Proteomics Using High-Efficiency Multiple-Capillary Liquid Chromatography with On-Line High-Performance ESI FTICR Mass Spectrometry, Anal. Chem., 2001, 73: 3011-3021.
[33] Andreas Premstaller, Herbert Oberacher, Wolfgang Walcher, et al., High-Performance Liquid Chromatography Electro-spray Ionization Mass Spectrometry Using Monolithic Capillary Columns for Proteomic Studies, Anal. Chem., 2001, 73: 2390-2396.
[34] Rachel R. Ogorzalek Loo, James D. Cavalcoli, Ruth A. VanBogelen, Charles Mitchell, et al, Virtual 2-D Gel Electrophoresis: Visualization and Analysis of the E. coliProteome by Mass Spectrometry, Anal. Chem., 2001, 73: 4063-4070.
[35] Steven Locke and Daniel Figeys, Techniques for the Optimization of proteomic Strategies Based on Head Column Stacking Capillary Electrophoresis, Anal. Chem., 2000, 72: 2684-2689.
[36] Pamela K. Jensen, Ljiljana Pas(?)a-Tolic', Gordon A. Anderson, Julie A. Horner, et al, Probing Proteomes Using Capillary Isoelectric Focusing-Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, 1999, 71: 2076-2084.
[37] Knut Wagner, Tasso Miliotis, Gyolrgy Marko-Varga, Rainer Bischoff, et al, An Automated On-Line Multidimensional HPLC System for Protein and Peptide Mapping with Integrated Sample Preparation, Anal. Chem., 2002, 74: 809-820.
[38] Hookeun Lee, Timothy J. Griffin, Steven P. Gygi, Beate Rist, et al, Development of a Multiplexed Microcapillary Liquid Chromatography System for High-Throughput Proteome Analysis, Anal. Chem., 2002, 74: 4353-4360.
[39] Zheru Zhang, Sergey Krylov, Edgar A. Arriaga, Robert Polakowski, et al, One-Dimensional Protein Analysis of an HT29 Human Colon Adenocarcinoma Cell, Anal. Chem., 2000, 72: 318-322.
[40] Tohru Natsume, Hiroshi Nakayama, Osten Jansson, Toshiaki Isobe, et al, Combination of Biomolecular Interaction Analysis and Mass Spectrometric Amino Acid Sequencing, Anal. Chem., 2000, 72: 4193-4198.
[41] Gerald Marie, Laurent Serani and Olivier Lapre′ vote, An On-Line Protein Digestion Device for Rapid Peptide Mapping by Electrospray Mass Spectrometry, Anal. Chem., 2000, 72: 5423-5430.
[42] Dirk A. Wolters, Michael P. Washburn and John R. Yates, An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics, Anal. Chem., 2001, 73: 5683-5690.
[43] Thierry Le Bihan, Devanon Pinto and Daniel Figeys, Nanoflow Gradient Generator Coupled with μ-LC-ESI-MS/MS for Protein Identification, Anal. Chem., 2001, 73: 1307-1315.
[44] 俞利荣，夏其昌等，人肝癌细胞系BEL-7404和正常肝细胞系L-02表达的蛋白质组双向凝胶电泳分析，科学通报，2000，45(2)：170-17．
[45] Li-rong Yu, Rong Zeng, Xiao-xia Shao, et al, Identification of differentially expressed proteins between human hepatoma and normal liver cell lines by two-dimensional electrophoresis and liquid chromatography-ion trap mass spectrometry, Electrophoresis, 2000, 21: 3058-3068.
[46] Youji Shimazaki, Seiichi Ohara, Takashi Manabe, Removal of specific protein spots on the patterns of non-denaturing two-dimensional electrophoresis using protein A agarose and antibodies, J. Biochem. Biophys. Methods, 1998, 37: 1-4.
[47] Haijun Sun, Yu-Ching E. Pan, Using native gel in two-dimensional PAGE for the detection of protein interactions in protein extract, J. Biochem. Biophys. Methods, 1999, 39: 143-151.
[48] Lan Huang, Min Shen, Igor Chernushevich, Alma L. Burlingame, et al, Identification and isolation of three proteasome subunits and their encoding genes from Trypanosoma brucei, Molecular and Biochemical Parasitology, 1999, 102: 211-223.
[49] Sarka Beranova-Giorgianni, Michael J. Pabst, Tara M. Russell, Francesco Giorgianni, et al, Preliminary analysis of the mouse cerebellum proteome, Molecular Brain Research, 2002, 98: 135-140.
[50] Yannicke Dauphin, Comparative studies of skeletal soluble matrices from some Scleractinian corals and Molluscs, International Journal of Biological Macromolecules, 2001, 28: 293-304.
[51] Anja Moller, Michael Soldan, Uwe Volker, Edmund Maser, Two-dimensional gel electrophoresis: a powerful method to elucidate cellular responses to toxic compounds, Toxicology, 2001,160:129-138.
[52] Seong Hwan Kim, Roman Vlkolinsky, Nigel Cairns, Michael Fountoulakis, et al, The reduction of NADH Ubiquinone oxidoreductase 24- and 75-kDa subunits in brains of patients with Down syndrome and Alzheimer's disease, Life Sciences, 2001, 68: 2741-2750.
[53] Peter W. Hewett, Identification of tumour-induced changes in endothelial cell surface protein expression: an in vitro model, The International Journal of Biochemistry & Cell Biology, 2001, 33: 325-335.
[54] Lirong Yu, Rong Zeng, Xiaoxia Shao, Nan Wang, et al, Identification of differentially expressed proteins between human hepatoma and normal liver cell lines by two-dimensional electrophoresis and liquid chromatography-ion trap mass spectrometry, Electrophoresis, 2000, 21: 2058-2068.
[55] Divis JM, Giddings JC, Statistical method for estimation of number of components from single complex chromatograms: theory, computer-based testing, and analysis of errors, Anal. Chem., 1985, 57: 2168-2177
[56] Giddings J C., Concepts and comparisons in multidimensional separation, J High Resolut. Chromatogr. Commun., 1987,10,319-323
[57] Liu Z., Patterson D.G., J r. Lee M L., Geometric approach to factor analysis for the estimation of orthogonality and practical peak capacity in comprehensive two-dimensional separation, Anal Chem , 1995 , 67(21) :3840-3845.
[58] Slonecker, P. J., Li X , Ridgway T H , Dorsey J G. Informational orthogonality of two-dimensional chromatographic separation, Anal Chem ,1996, 68 : 682-689.
[59] Murphy R E , Schure M R , Foley J P, Effect of sampling rate on resolution in comprehensive two-dimensional liquid chromatography, Anal Chem , 1998 , 70 :1585-1594.
[60] Issaq, H.J., Chan, K.C., Janini, G.M., Conrads, T.P., Veenstra, T.D. Multidimensional separation of peptides for effective proteomic analysis, J. Chromatogr. B, 2005, 817, 35-47.
[61] Bushey, M.M. , Jorgenson, J.W. , Automated instrumentation for comprehensive two-dimensional high-performance liquid chromatography of proteins, Anal.Chem., 1990, 62,161-167.
[62] Holland, L.A., Jorgenson, J.W., Separation of nanoliter samples of biological amines by a comprehensive two-dimensional microcolumn liquid chromatography system, Anal.Chem., 1995, 67, 3275-3283.
[63] Opiteck, GJ., Lewis, K.C., Jorgenson, J.W., Comprehensive on-line LC/LC/MS of proteins, Anal. Chem., 1997, 69,1518-1524.
[64] Opiteck, G.J.; Jorgenson, J.W. Two-dimensional SEC/RPLC coupled to mass spectrometry for the analysis of peptides, Anal.Chem., 1997, 69, 2283-2291.
[65] Wagner, K., Racaityte, K., Unger, K.K., Miliotis, T., Edhholm., L.E., Bischoff, R., Marko-varga,G., Protein mapping by two-dimensional high performance liquid chromatography, J. Chromatogr. A, 2000, 893, 293-305.
[66] Wagner, K.; Miliotis, T., Marko-varga, G., Bischoff, R., Unger, K.K. An automated on-linemultidimensional HPLC system for protein and peptide mapping with integrated sample preparation, Anal. Chem., 2002, 74, 809-820.
[67] Vissers, J.P.C., van Soest, R.E.J., Chervet, J-P., Cramers, C.A. Two-dimensional capillary liquid chromatography based on microfractionation, J. Microcolumn Sep., 1999, 11, 277-286.
[68] Wolters, D.A., Washburn, M.P., Yates III, J.R. An automated multidimensional protein identification technology for shotgun proteomics, Anal.Chem., 2001, 73, 5683-5690.
[69] Liu H., Lin D., Yates, JR III.,Multidimensional separations for protein/peptide analysis in the post-genomic era, Bio Technique, 2002, 32(4), 898-902.
[70] Zhang, Z., Smith, D.L., Smith, J.B. Multiple separations facilitate identification of protein variants by mass spectrometry, Proteomics, 2001, 1,1001-1009.
[71]Richter, R., Schulz Knappe, P., Schrader, M., Standker, L., Jurgens, M., Tammen, H., Forssmann, W.G. Composition of the peptide fraction in human blood plasma: database of circulating human peptides, J.Chromatopr.B, 1999,726, 25-35.
[72] Chen, Y., Wall, D., Lubman, D.M. Rapid identification and screening of proteins from whole cell lysates of human erythroleukemia cells in the liquid phase, using non-porous reversed phase high-performance liquid chromatography separations of proteins followed by multi-assisted laser desorption/ionization mass spectrometry analysis and sequence database searching, Rappid. Commun. Mass. Spectrom., 1998,12,1994-2003.
[73] Apffel, A., Chakel, J.A., Hancock, W.S., Souders, C, M'Timkulu, T., Pungor J.E. Application of multidimensional affinity high-performance liquid chromatography and electrospray ionization liquid chromatography-mass spectrometry to the characterization of glycosylation in single-chain plasminogen activator: Initial results, J.Chromatpgr.A, 1996,750, 35-42.
[74]Hsieh, Y. L. F., Wang, H.; Elicone, C., Mark, J., Martin, S. A., Regnier, F. Automated analytical system for the examination of protein primary structure, Anal. Chem., 1996, 68, 3, 455-462.
[75] Geng, M., Ji, J., Regnier, F.E. Signature-peptide approach to detecting proteins in complex mixtures, J. Chromatogr. A, 2000, 870, 295-313.
[76] Riggs, L.; Sioma, C.; Regnier, F.E. Automated signature peptide approach for proteomics, J. Chromatogr. A., 2001, 924, 359-368.
[77] Han, D.K. , Eng, J. , Zhou, H. , Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry, Nat. Biotechnol., 2001,19, 946-951.
[78]Goshe, M. B., Veenstra, T. D., Panisko, E. A., Conrads,T. P., Angell, N. H., Smith, R. D. Phosphoprotein isotope-coded affinity tags: Application to the enrichment and identification of low-abundance phosphoproteins, Anal. Chem., 2002, 74, 607-616.
[79] Ficarro, S.B., McCleland, M.L., Stukenberg, P.T., Burke, D.J., Ross, M.M., Shabanowitz, J.; Hunt, D.F.; White, F.M. Phosphoproteome analysis by mass sepectrometry and its application to saccharomyces cerevisiae, Nat. Biotechnol., 2002, 20, 301-305.
[80] Gygi, S. P., Rist, B., Griffin, T. J., Eng, J., Aebersold, R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags, J. Proteome Res., 2002,1, 47-54.
[81]Shen,Y., Jacobs, J.M., Camp II, D.G., Fang, R., Moore, R.J., Smith, R.D., Xiao,W., Davis, R.W. , Tompkins, R.G. Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome, Anal. Chem., 2004, 76,1134-1144.
[82] Jin, W.H., Dai, J, Li, S.J., Xia, Q.C., Zou, H.F., Zeng, R., Human Plasma Proteome Analysis by Multidimensional Chromatography Prefractionation and Linear Ion Trap Mass Spectrometry Identification, J. Proteome Res., 2005, 4, 613-619.
[83] Tu, C.J., Dai, J., Li, S.J., Sheng, Q.H., Deng, W.J., Qia, Q.C., Zeng, R., High-Sensitivity Analysis of Human Plasma Proteome by Immobilized Isoelectric Focusing Fractionation Coupled to Mass Spectrometry Identification, J. Proteome Res., 2005, 4,1265-1273.
[84] Li, R.X., Zhou, H., Li, S.J., Sheng, Q.H., Qia, Q.C., Zeng, R., Prefractionation of Proteome by Liquid Isoelectric Focusing Prior to Two-Dimensional Liquid Chromatography Mass Spectrometric Identification, J. Proteome Res., 2005, 4, 1256-1264.
[85] Wall, D. B., Kachman, M. T., Gong, S., Hinderer, R., Parus, S., Misek, D. E., Hanash, S. M., Lubman, D. M., Isoelectric Focusing Nonporous RP HPLC: A Two-Dimensional Liquid-Phase Separation Method for Mapping of Cellular Proteins with Identification Using MALDI-TOF Mass Spectrometry, Anal. Chem., 2000, 72,1099-1111.
[86] Kachman, M. T., Wang, H., Schwartz, D. R., Cho, K. R., Lubman, D. M. A 2-D Liquid Separations/Mass Mapping Method for Interlysate Comparison of Ovarian Cancers., Anal. Chem., 2002, 74,1779-1791.
[87] Zhu, K., Kim, J., Yoo, C, Miller, F. R., Lubman, D. M. High Sequence Coverage of Proteins Isolated from Liquid Separations of Breast Cancer Cells Using Capillary Electrophoresis-Time-of-Flight MS and MALDI-TOF MS Mapping, Anal. Chem., 2003, 75, 6209-6217.
[88] Yan, F., Subramanian, B., Nakeff, A., Barder, T. J., Parus, S. J., Lubman, D. M. A Comparison of Drug-Treated and Untreated HCT-116 Human Colon Adenocarcinoma Cells Using a 2-D Liquid Separation Mapping Method Based upon Chromatofocusing PI Fractionation, Anal. Chem., 2003, 75, 2299-2308.
[89] Zhu, Y., Lubman, D.M. Narrow-band fractionation of proteins from wholecell lysates using isoelectric membrane focusing and nonporous reversed-phase separations, Electrophoresis, 2004, 25, 949-958.
[90] Chen, J., Balgley, B. M., DeVoe, D. L., Lee, C. S. Capillary Isoelectric Focusing-Based Multidimensional Concentration/Separation Platform for Proteome Analysis, Anal. Chem., 2003, 75,3145-3152.
[91] Mohan, D., Pasˇa-Tolic', L., Masselon, C. D., Tolic', N., Bogdanov, B., Hixson, K. K., Smith, R. D., Lee, C. S. Integration of Electrokinetic-Based Multidimensional Separation/Concentration Platform with Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry for Proteome Analysis of Shewanella oneidensis, Anal. Chem., 2003, 75, 4432-4440.
[92] Wang, Y., Balgley, B.M., Rudnick, P.A., Evans, E.L., DeVoe, D.L., Lee, C.S. Integrated Capillary Isoelectric Focusing/Nano-reversed Phase Liquid Chromatography Coupled with ESI-MS for Characterization of Intact Yeast Proteins, J. Proteome Res., 2005, 4, 36-42.
[93] Meng, F., Cargile, B. J., Patrie, S. M., Johnson, J. R., McLoughlin, S. M., Kelleher, N. L. Processing Complex Mixtures of Intact Proteins for Direct Analysis by Mass Spectrometry, Anal. Chem., 2002, 74, 2923-2929.
[94] Meng, F., Du, Y., Miller, L. M., Patrie, S. M., Robinson, D. E., Kelleher, N. L. Molecular-Level Description of Proteins from Saccharomyces cerevisiae Using Quadrupole FT Hybrid Mass Spectrometry for Top Down Proteomics, Anal. Chem., 2004, 76, 2852-2858.
[1] Shaw MM, Riederer BM, Sample preparation for two-dimensional gel electrophoresis, Proteomics 2003, 3:1408-1417.
[2] Chertov O, Biragyn A, Kwak LW, Simpson JT, Boronina T, Hoang VM, Prieto DA, Conrads TP, Veenstra TD, Fisher RJ, Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry Proteomics, 2004, 4:1195-1203
[3] Tastet C, Charmont S, Chevallet M, Luche S, Rabilloud T, Structure-efficiency relationships of zwitterionic detergents as protein solubilizers in two-dimensional electrophoresis, Proteomics, 2003, 3:111-121.
[4] Luche S, Santoni V, Rabilloud T, Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis, Proteomics, 2003, 3:249-253.
[5] Henningsen R., Gale B.L., Straub K.M., DeNagel D.C., Application of zwitterionic detergents to the solubilization of integral membrane proteins for two-dimensional gel electrophoresis and mass spectrometry, Proteomics, 2002, 2(11): 1479-1488.
[6] Molloy M.P., Phadke N.D., Maddock J.R., Andrews P.C., Two-dimensional electrophoresis and peptide mass fingerprinting of bacterial outer membrane proteins, Electrophoresis, 2001, 22: 1686-1696.
[7] Molloy M.P., Herbert B.R., Slade M.B., Rabilloud T., Nouwens A.S., Williams K.L.,Gooley A.A., Proteomic analysis of the Escherichia coli outer membrane, Eur. J. Biochem., 2000, 267: 2871.
[8] Liberatori S., Bini L., De Felice C, Magi B., Marzocchi B., Raggiaschi R., Pallini V., Bracci R., Acute-phase proteins in perinatal human plasma, Electrophoresis, 1997,18: 520-526.
[9] O'Connell K.L., Stults J.T., Identification of mouse liver proteins on two-dimensional electrophoresis gels by matrix-assisted laser desorption ionization mass spectrometry of in situ enzymatic digests, Electrophoresis, 1997,18: 349-359.
[10] Sarto C, Marocchi A., Sanchez J-C, Giannone D., Frutiger S., Golaz O., Wilkins M.R., Doro G., Cappellano F., Hughes G., Hochstrasser D.F., Mocarelli P., Renal cell carcinoma and normal kidney protein expression, Electrophoresis, 1997,18: 599-604.
[11] Garfin DE, Two-dimensional gel electrophoresis: an overview, Trend in Analytical Chemistry, 2003, 22:263-272.
[12] Qu, Y., Moons, L., Vandesande, F., Determination of serotonin, catecholamins and their metabolites by direct injection of supernatants from chicken brain tissue homogenate using liquid chromatography with electrochemical detection . J. Chromatogr. B. 1997, 704, 351-358.
[13] Wei J, Sun J, Yu W, Jones A, Oeller P, Keller M, Woodnutt G, Short JM, Global proteome discovery using an online three-dimensional LC-MS/MS, J. Proteome Research, 2005, 4:801-808.
[14] Jin, W.H., Dai, J., Li, S. J., Xia, Q.C., Zou, H.F., Zeng, R., Human Plasma Proteome Analysis by Multidimensional Chromatography Prefractionation and Linear Ion Trap Mass Spectrometry Identification, J. Proteome Research, 2005, 4: 613-619.
[15] Tyan, Y. C, Wu, H.Y., Lai, W. W., Su, W. C, Liao, P. C, Proteomic Profiling of Human Pleural Effusion Using Two-Dimensional Nano Liquid Chromatography Tandem Mass, J. Proteome Research, 2005, 4:1274-1286.
[16] Ryden L, Carlsson J, in: Janson J, Ryden L (Eds.), High Resolution Methods, and Applications, VCH, Uppsala, 1989, pp. 252-274.
[17] Bae SH, Harris AG, Hains PG, Chen H, Garfin DE, Hazell SL, Paik YK, Walsh BJ, Cordwell SJ, Strategies for the enrichment and identification of basic proteins in proteome of projects, Proteomics, 2003, 3:569-579.
[18] Kline TR, Pang J, Hefta SA, Opiteck GJ, Kiefer SE, Scheffler JE, A high-yield method to extract peptides from rat brain tissue, Anal. Biochem., 2003, 315:183-188.
[1] Anderson, N. G., Matheson, A., Anderson, N. L. Back to the future: the human protein index (HPI) and the agenda for post-proteomic biology, Proteomics, 2001,1, 3-12.
[2] Hanash S. M., Biomedical applications of two-dimensional electrophoresis using immobilized pH gradients: Current status, Electrophoresis, 20002,1,1202-1209.
[3] Shevchenko, A., Wilm, M., Vorm, O., Mann, M., Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels, Anal. Chem. 1996, 68, 850-858.
[4] Anja Moller, Michael Soldan, Uwe Volker, Edmund Maser, Two-dimensional gelelectrophoresis: a powerful method to elucidate cellular responses to toxic compounds, Toxicology, 2001, 160: 129-138.
[5] Adamczyk, M., Gebler, J. C, Selective analysis of phosphopeptides within a proteinmixture by chemical modification, reversible biotinylation and mass spectrometry, J. Rapid Commun. Mass Spectrom 2001,15,1481-1488.
[6] Greenough, C.,Jenkins, R.E.,Kitteringham, N. R., Pirmohamed, M., Park, B. K., Pennington, S. R A method for the rapid depletion of albumin and immunoglobulin from human plasma, Proteomics 2004, 4, 3107-3111.
[7] R. Pieper, C.L. Gatlin, A.J. Makusky, P.S.,et al, Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome, Proteomics,2003, 3, 422-432.
[8] Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F, White F.M., Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae, Nat. Biotechnol., 2002, 20, 301-305.
[9] Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat. Biotechnol. 1999,17, 994-999.
[10] Badock, V., Steinhusen, U., Bommert, K., Otto, A., Prefractionation of protein samples for proteome analysis using reversed-phase high-performance liquid chromatography, Electrophoresis, 2001, 22, 2856-2864.
[11] Bergh, G. V., Clerens, S., Vandesande, F., Arckens, L., Reversed-phase high-performance liquid chromatography prefractionation prior to two-dimensional difference gel electrophoresis and mass spectrometry identifies new differentially expressed proteins between striate cortex of kitten and adult cat, Electrophoresis, 2003, 24,1471-1481.
[12] Butt, A., Davison, M. D., Smith, G. J., Young, J. A., Gaskell, S. J.,Oliver, S. G., Beynon, R. J., Chromatographic separations as a prelude to two-dimensional electrophoresis in proteomics analysis, Proteomics, 2001, 1, 42-53.
[13] Bier, M., Recycling isoelectric focusing and isotachophoresis, Electrophoresis 1998, 19, 1057-1063.
[14] Hannig, K., New aspects in preparative and analytical continuous free-flow cell electrophoresis, Electrophoresis 1982, 3, 235-243.
[15] Margolis J., Corthals G., Horvath Z.S., Preparative reflux electrophoresis, Electrophoresis 1995,16, 98-100.
[16] Horvath, Z. S., Gooley,A. A., Wrigley, C. W., Margolis, J., Williams, K.L. Preparative affinity membrane electrophoresis, Electrophoresis 1996,17, 224-226.
[17] P.G. Righetti, A. Castagna, B. Herbert, F. Reymond, J.S. Rossier, Prefractionation techniques in proteome analysis, Proteomics, 2003, 3, 1397-1407.
[18] H.R. Mahler, E.H.Cordes, Biological Chemistry, Harper &Row, New York 1971, pp. 441-461.
[19] Qu, Y., Moons, L., Vandesande, F. Determination of serotonin, catecholamins and their metabolites by direct injection of supernatants from chicken brain tissue homogenate using liquid chromatography with electrochemical detection . J. Chromatogr. B. 1997, 704, 351-358.
[20] G. Winkler, P. Wolschann, P. Briza, F.X. Heinz, C.J. Kunz, J. Chromatogr., 1985, 347: 83.
[21] Yeldandi A., Rao M., Reddy J., Mutation Research-fund Amental and Molecular Mechanisms of Muta Genesis, 2000,448:159-166.
[22] G. Kirby, C. Wolf, G. Neal, D. Judahdj, C. Henderson, P. Srivatanakulp, C. Wild, Carcinogenesis, 1993,14: 2613-2619.
[23] J. Yu, S. Yun, J. Lim, H. Kim, K. Kim, Proteome analysis of rat pancreatic acinar cells: Implication for cerulein-induced acute pancreatitis, Proteomics, 2003, 3: 2446-2453.
[24] G. Chen, T. Gharib, C. Huang, D. Thomas, K. Shedden, J. Taylor, S. Kardia, D. Misek, T. Giordano, M. Iannettoni, M. Orringer, S. Hanash, D. Beer, Proteomic analysis of lung adenocarcinoma: Identification of a highly expressed set of proteins in tumors, Clinical Cancer Research, 2002, 8: 2298-2305.
[25] I. Corbin, Y. Gong, M. Zhang, G. Minuk, Proliferative and nutritional dependent regulation of glyceraldehyde-3-phosphate dehydrogenase expression in the rat liver, Cell Proliferation, 2002, 35: 173-182.
[26] D. Goldenberg, S. Ayesh, T. Schneider, O. Pappo, O. Jurim, A. Eid, Y. Fellig, T. Dadon, I. Ariel, N. de Groot, A. Hochberg, E. Galun, Mol. Carcinogen, 2002 33,:113-117.
[1] Badock, V., Steinhusen, U.> Bommert, K., Otto, A.,Prefractionation of protein samples for proteome analysis using reversed-phase high-performance liquid chromatography, Electrophoresis 2001, 22, 2856-2864.
[2] Anderson, N. G., Matheson, A., Anderson, N. L. Back to the future: the human protein index (HPI) and the agenda for post-proteomic biology, Proteomics, 2001,1, 3-12
[3] Shevchenko, A.? Wilm, M.; Vorm, O., Mann, M. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels, Anal. Chem. 1996, 68, 850-858.
[4] Shaw, M. M., Riederer, B. M. Sample preparation for two-dimensional gel electrophoresis, Proteomics 2003, 3,1408-1417.
[5] Corthals, G. L., Wasinger, V. C.? Hochstrasser, D. F., Sanchez, J. C, The dynamic range of protein expression: A challenge for proteomic research, Electrophoresis, 2000, 21, 1104-1115.
[6] Wasinger, V. C., Pollack, J. D., Humphery, S. I.,The proteome of mycoplasma genitalium chaps-soluble component, Eur. J. Biochem. 2000, 267,1571-1582.
[7] Shen, Y. F., Jacobs, J. M., Camp, D. G., II, Fang, R. H., Moore, R. J., Smith, R. D., Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome.Anal. Chem. 2004, 76,1134-1144.
[8] Wu, C. C., MacCoss, M. J., Howell, K. E., Yates, J. R. III, A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 2003, 21, 532-538.
[9] McDonald, W. H., Ohi, R., Miyamoto, D. T., Mitchison, T. J., Yates, J. R. III, Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: single-dimension LC-MS/MS, 2-phase MudPIT, and 3-phase MudPIT, Int. J. Mass Spectrom. 2002,219, 245-251.
[10] Washburn, M. P., Wolters, D., Yates, J. R. III, Large-scale analysis of the yeast proteome by multidimensional protein identification technology .Nat. Biotechnol. 2001, 19, 242-247.
[11] Peng, J. M., Elias,J. E., Thoreen, C. C., Licklider, L. J., Gygi, S. P. Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. J. Proteome Res. 2003, 2, 43-50.
[12] Fujii, K., Nakano, T., Kawamura, T., Usui, F., Bando, Y., Wang, R., Nishimura, T. Multidimensional Protein Profiling Technology and Its Application to Human Plasma Proteome. J. Proteome Res. 2004, 3, 712-718.
[13] Dreger, M., Subcellular proteomics, Mass Spec Rev 2003, 22, 27-56
[14] N. Karoline Scheficer, Scott W. Millerc, Amy K. Carrollc, Christen Andersonc, et al, Two-dimensional electrophoresis and mass spectrometric identification of mitochondrial proteins from an SH-SY5Y neuroblastoma cell line, Mitochondrion, 2001,1: 161-179
[15] Bier, M., Recycling isoelectric focusing and isotachophoresis, Electrophoresis 1998, 19, 1057-1063.
[16] Hannig, K., New aspects in preparative and analytical continuous free-flow cell electrophoresis, Electrophoresis 1982, 3, 235-243.
[17] Margolis J., Corthals G., Horvath Z.S., Preparative reflux electrophoresis, Electrophoresis 1995,16, 98-100.
[18] Horvath, Z. S., Gooley, A. A., Wrigley, C. W., Margolis, J., Williams, K.L. Preparative affinity membrane electrophoresis, Electrophoresis 1996,17, 224-226.
[19] Van den Bergh G., Clerens, S., Vandesande, F., Arckens, L., Reversed-phase high-performance liquid chromatography prefractionation prior to two-dimensional difference gel electrophoresis and mass spectrometry identifies new differentially expressed proteins between striate cortex of kitten and adult cat, Electrophoresis, 2003, 24, 1471-1481.
[20] Butt, A., Davison, M. D., Smith, G. J., Young, J. A., Gaskell, S. J.,Oliver, S. G., Beynon, R. J., Chromatographic separations as a prelude to two-dimensional electrophoresis in proteomics analysis, Proteomics, 2001,1, 42-53.
[21] Jacobs, J. M., Mottaz, H. M., Yu, L. R., Anderson, D. J., Moore, R. J., Chen, W.N. U., Auberry, K. J., Strittmatter, E. F., Monroe, M. E., hrall, B. D., Camp, D. G. II, Smith, R. D. J. Proteome Res. 2004, 3, 68-75.
[22] Adamczyk, M., Gebler, J. C.Wu, Selective analysis of phosphopeptides within a protein mixture by chemical modification, reversible biotinylation and mass spectrometry, J. Rapid Commun. Mass Spectrom 2001,15,1481-1488.
[23] Greenough, C, Jenkins, R.E., Kitteringham, N. R., Pirmohamed, M., Park, B. K., Pennington, S. R A method for the rapid depletion of albumin and immunoglobulin from human plasma, Proteomics 2004, 4, 3107-3111.
[24] Pieper R., Gatlin C.L., Makusky A.J., et al, Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome, Proteomics,2003, 3, 422-432.
[25] Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F, White F.M., Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae, Nat. Biotechnol., 2002, 20, 301-305.
[26] Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat. Biotechnol. 1999,17, 994-999.
[27] Qu, Y., Moons, L., Vandesande, F. Determination of serotonin, catecholamins and their metabolites by direct injection of supernatants from chicken brain tissue homogenate using liquid chromatography with electrochemical detection . J. Chromatogr. B. 1997, 704, 351-358.
[28] Zhang, X. M., Huang, S. Single step on-column frit making for capillary high-performance liquid chromatography using sol-gel technology J. Chromatogr. A 2001, 910,13-18.
[29] Mao, Y., Zhang, X. M. Comprehensive two-dimensional separation system by coupling capillary reverse-phase liquid chromatography to capillary isoelectric focusing for peptide and protein mapping with laser-induced fluorescence detection Electrophoresis 2003, 24, 3289-3295.
[30] Yang, X. H., Zhang, X. M., Li, A. Z., Zhu, S. Y., Huang, Y. P. Comprehensive two-dimensional separations based on capillary high-performance liquid chromatography and microchip electrophoresis.Electrophoresis 2003, 24,1451-1457.
[31] Zhang, J., Hu, H. L., Gao, M. X., Yang, P. Y., Zhang, X. M. Comprehensive two-dimensional chromatography and capillary electrophoresis coupled with tandem time-of-flight mass spectrometry for high-speed proteome analysis.Electrophoresis 2004, 25, 2374-2383.
[32] Wang, Y., Zhang, J., Liu, C. L., Gu, X., Zhang, X. M. Nano-flow multidimensional liquid chromatography with electrospray ionization time-of-flight mass spectrometry for proteome analysis of hepatocellular carcinoma Analytica Chimica Acta, 2005, 530, 227-235.
[33] Bordin, G., Cordeiro Raposo, F., Calle, B. de la, Rodriguez, A.R. Identification and quantification of major bovine milk proteins by liquid chromatography. J. Chromatogr. A, 2001, 928, 63-76.
[34] Ferreira, I.M.P.L.V.O., Cacote, H. Detection and quantification of bovine, ovine and caprine milk percentages in protected denomination of origin cheeses by reversed-phase high-performance liquid chromatography of beta-lactoglobulins.J. Chromatogr. A, 2003, 1015,111-118.
[35] Merbel, N. C. van de, Mentink, C. J.A.L., Hendriks, G.,Wolffenbuttel, B.H.R. Liquid chromatographic method for the quantitative determination of iV-carboxymethyllysine in human plasma proteins. J. Chromatogr. B, 2004, 808,163-168.
[36] Bu¨nger, H., Kaufner, L., Pison, U. Quantitative analysis of hydrophobic pulmonary surfactant proteins by high-performance liquid chromatography with light-scattering detection J. Chromatogr. A, 2000, 870 363-369.
[37] Toorop, R.M., Murch, S.J., Ball, R.O., Development of a rapid and accurate method for separation and quantification of myofibrillar proteins in meat, Food Res. International, 1997, 30, 619-627.
[38] Zhu, H.N., Pan, S.Q., Gu, S., Bradbury, E.M. ,Chen, X. Amino acid residue specific stable isotope labeling for quantitative proteomics., Rapid Commun. Mass Spectrom, 2002,16, 2115-2123.
[39] Gu, S., Du, Y.C., Chen, J., Liu, Z.H., Bradbury, E.M., Hu, C.A., Chen, X. Large-Scale Quantitative Proteomic Study of PUMA-Induced Apoptosis Using Two-Dimensional Liquid Chromatography-Mass Spectrometry Coupled with Amino Acid-Coded Mass Tagging, J. Proteome Res. 2004, 3,1191-1200.
[40] Gu, S., Liu, Z.H., Pan, S.Q., Jiang, Z.Y., Lu, H.M., Bradbury, E.M., Hu, C.A., Chen, X. Global Investigation of p53-induced Apoptosis Through Quantitative Proteomic Profiling Using Comparative Amino Acid-coded Tagging; Molecular & Cellular Proteomics, 2004, 3, 998-1008.
[41] Gao, M.X., Jin, H., Yang, P.Y., Zhang, X.M. Chromatographic prefractionation prior to two-dimensional electrophoresis and mass spectrometry identifies: Application to the complex proteome analysis in rat liver, Analytica Chimica Acta, 2005, 553, 83-92.
[42] Hochstrasser, D. E, Wilkins, M. R., Williams, K. L., Appel,R. D., Hochstrasser, D. E (Eds.), Proteome Research: New Frontiers in Functional Genomics, Springer, New York 1997,pp. 187.
[43] Tang, Z.Y., Sun, F.X., Tian, J., Ye, S.L, Liu, Y.K., Liu, K.D., Xue, Q., Chen, J., Xia, J.L., Qin, L.X., Sun, H.C., et al, World J Gastroenterol 2001, Oct 7(5):597-603.
[44] Sun, F.X., Tang, Z.Y., Liu, K.D., Ye, S.L., Xue, Q., Zhonghua Yixue Zazhi, 1995,75:673-685.
[45] Sun, F. X., Tang, Z,Y., Liu, K.D., Ye, S.L., Xue, Q., Gao, D,M,, Ma, Z.C., Int J Cancer, 1996,66:239-245
[46] 汤钊猷，肝癌转移复发的基础与临床，上海科技教育出版社，2003．
[47] Sam Hanash, Building a foundation for the human proteome organization,J. Proteome Res., 2004, 3, 197-199.
[48] Lescuyer, P., Hochstrasser, D.F., Sanchez, J.C., Comprehensive proteome analysis by chromatographic protein prefractionation, Electrophoresis, 2004, 25, 1125-1135.
[1] Venter J C, Adams M D, Myers E W, Li P W, Mural R J, Sutton G G, Smith H O, Yandell M, Evans C A, Holt R A, et al .The sequence of human genome, Science, 2001,291 : 1304-1351.
[2] Lander E S, Linton L M, Birren B, Nusbaum C, Zody M C ,Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, FunkeR, Gage D, et al, Initial sequencing and analysis of the human genome, Nature, 2001,409 : 860-921.
[3] Naaby-Hansen S, Waterfield M D, Cramer R., Proteomics-post-genomic cartography to understand gene function, Trends in Pharmacological Sciences, 2001,22 (7) : 376-384.
[4] 贺福初，蛋白质组研究—后基因组时代的生力军，科学通报，1999，44(2)：113-122．
[5] 张养军，蔡耘，王京兰，李晓海，钱小红，蛋白质组学研究中的色谱分离技术，色谱，2003，21，120-26．
[6] Chen H, Horvath C, High-speed high-performance liquid chromatography of peptides and proteins, J chromatography A, 1995, 705: 3-20.
[7] Dolnik V, Hutterer KM, Capillary electrophoresis of proteins 1999-2001, Electrophoresis, 2001, 22: 4163-4178.
[8] Giddings JC, Concepts and comparisons in multidimensional separation, J High Resoluti. Chromatogr. Commun., 1987, 10: 319-323.
[9] Divis JM, Giddings JC, Statistical method for estimation of number of components from single complex chromatograms: theory, computer-based testing, and analysis of errors, Anal. Chem. 1985, 57: 2168-2177.
[10] Divis JM, Giddings JC, Statistical method for estimation of number of components from single complex chromatograms: application to experimental chromatograms, Anal. Chem. 1985, 2178-2185.
[11] Jinzhi Chen, Cheng S. Lee, Yufeng Shen, Richard D. Smith, Eric H Baehrecke, Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation, electrophoresis, 2002, 23: 3143-3148.
[12] Hongbin Liu, Dayin Lin, John R. Yate Ⅲ, Multidimensional separations for protein/peptide analysis in the post-genomic era, Biotechniques, 2002, 32, 4: 898-911.
[13] 张丽华，张维冰，张玉奎，马场嘉信，多维高效液相色谱／毛细管电泳模式在蛋白质研究中的应用，色谱，2003，21，1：32-37．
[14] Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., Yates, J. R. Ⅲ, Direct analysis of protein complexes using mass spectrometry Nat. Biotechnol.,1999, 17, 676-682.
[15] Wu, C. C., MacCoss, M. J., Howell, K. E., Yates, J. R. Ⅲ,A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol., 2003, 21, 532-538.
[16] Washburn, M. P., Wolters, D., Yates, J. R. Ⅲ, Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol., 2001,19, 242-247.
[17] Shen, Y., Jacobs, J. M., Camp, D. G., Ⅱ, Fang, R., Moore, R. J., Smith, R. D., Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal. Chem., 2004, 76, 1134-1144.
[18] Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., Gygi, S. P., Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. J. Proteome Res., 2003, 2, 43-50.
[19] Fujii, K., Nakano, T., Kawamura, T., Usui, F., Bando, Y., Wang, R., Nishimura, T., Multidimensional Protein PrOfiling Technology and Its Application to Human Plasma Proteome. J. Proteome Res., 2004, 3, 712-718.
[20] Han, D. K., Eng, J., Zhou, H., Aebersold, R., Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol., 2001, 19, 946-951.
[21] VerBerkmoes, N. C., Bundy, J. L., Hauser, L., Asano, K. G., Razumovskaya, J., Larimer, F., Hettich, R. L., Stephenson, J. L. Jr., Integrating "Top-Down" and "Bottom-Up" Mass Spectrometric Approaches for Proteomic Analysis of Shewanella oneidensis. J. Proteome Res., 2002, 1,239-252.
[22] Gygi, S. P., Rist, B., Griffin, T. J., Eng, J., Aebersold, R., Proteome Analysis of Low-Abundance Proteins Using Multidimensional Chromatography and Isotope-Coded Affinity Tags. J. Proteome Res., 2002,1, 47-54.
[23] Wu, S.-L., Choudhary, G., Ramstrom, M., Bergquist, J., Hancock, W. S. Evaluation of Shotgun Sequencing for Proteomic Analysis of Human Plasma Using HPLC Coupled with Either Ion Trap or Fourier Transform Mass Spectrometry J. Proteome Res., 2003, 2, 383-393.
[24] Mann, M., Jensen, O. N., Proteomic analysis of post-translational modifications. Nat. Biotechnol., 2003, 2, 255-261.
[25] MacCoss, M. J., McDonald, W. H., Saraf, A., Sadygov, R., Clark, J. M., Tasto, J. J., Gould, K. L., Wolters, D., Washburn, M., Weiss, A., Clark, J. I., Yates, J. R. III, Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci., U.S.A., 2002, 99, 7900-7905.
[26] Choudhary, G., Wu, S.L., Shieh, P., Hancock, W. S., Multiple Enzymatic Digestion forEnhanced Sequence Coverage of Proteins in Complex Proteomic Mixtures Using Capillary LC with Ion Trap MS/MS. J. Proteome Res., 2003, 2, 59-67.
[27] Wall, D. B., Kachman, M. T., Gong, S., Hinderer, R., Parus, S., Misek, D. E., Hanash, S. M., Lubman, D. M., Isoelectric Focusing Nonporous RP HPLC: A Two-Dimensional Liquid-Phase Separation Method for Mapping of Cellular Proteins with Identification Using MALDI-TOF Mass Spectrometry, Anal. Chem., 2000, 72,1099-1111.
[28] Kachman, M. T., Wang, H., Schwartz, D. R., Cho, K. R., Lubman, D. M., A 2-D Liquid Separations/Mass Mapping Method for Interlysate Comparison of Ovarian Cancers, Anal. Chem., 2002, 74,1779-1791.
[29] Zhu, K., Kim, J., Yoo, C, Miller, F. R., Lubman, D. M., High Sequence Coverage of Proteins Isolated from Liquid Separations of Breast Cancer Cells Using Capillary Electrophoresis-Time-of-Flight MS and MALDI-TOF MS Mapping, Anal. Chem., 2003, 75, 6209-6217.
[30] Yan, F., Subramanian, B., Nakeff, A., Barder, T. J., Parus, S. J., Lubman, D. M., A Comparison of Drug-Treated and Untreated HCT-116 Human Colon Adenocarcinoma Cells Using a 2-D Liquid Separation Mapping Method Based upon Chromatofocusing PI Fractionation, Anal. Chem., 2003, 75, 2299-2308.
[31] Zhu, Y., Lubman, D.M., Narrow-band fractionation of proteins from wholecell lysates using isoelectric membrane focusing and nonporous reversed-phase separations Electrophoresis, 2004, 25, 949-958.
[32] Chen, J., Balgley, B. M., DeVoe, D. L., Lee, C. S., Capillary Isoelectric Focusing-Based Multidimensional Concentration/Separation Platform for Proteome Analysis, Anal. Chem., 2003, 75, 3145-3152.
[33] Mohan, D., PasVTolic', L., Masselon, C. D., Tolic', N., Bogdanov, B., Hixson, K. K., Smith, R. D., Lee, C. S., Integration of Electrokinetic-Based Multidimensional Separation/Concentration Platform with Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry for Proteome Analysis of Shewanella oneidensis, Anal. Chem., 2003, 75, 4432-4440.
[34] Wang, Y., Balgley, B.M., Rudnick, P.A., Evans, E.L., DeVoe, D.L., Lee, C.S., Integrated Capillary Isoelectric Focusing/Nano-reversed Phase Liquid Chromatography Coupled with ESI-MS for Characterization of Intact Yeast Proteins, J. Proteome Res., 2005, 4, 36-42.
[35] Meng, F., Cargile, B. J., Patrie, S. M., Johnson, J. R., McLoughlin, S. M., Kelleher, N. L., Processing Complex Mixtures of Intact Proteins for Direct Analysis by MassSpectrometry, 2002, Anal. Chem., 74, 2923-2929.
[36] Meng, F., Du, Y., Miller, L. M., Patrie, S. M., Robinson, D. E., Kelleher, N. L.,Molecular-Level Description of Proteins from Saccharomyces cerevisiae Using Quadrupole FT Hybrid Mass Spectrometry for Top Down Proteomics, Anal. Chem., 2004,76, 2852-2858.
[37] Dogruel, D., Williams, P., Nelson, R.W., Rapid Tryptic Mapping Using Enzymically Active Mass Spectrometer Probe Tips, Anal. Chem., 1995, 67,4343-4348.
[38] Hsieh, Y.L.F., Wang, H.Q., Elicone, C, Mark, J., Martin, S.A., Regnier, F., Automated Analytical System for the Examination of Protein Primary Structure, Anal. Chem., 1996, 68, 455-462.
[39] Sakai-Kato, K., Kato, M., Toyo'oka, T., On-Line Trypsin-Encapsulated Enzyme Reactor by the Sol-Gel Method Integrated into Capillary Electrophoresis, Anal. Chem., 2002, 74, 2943-2949.
[40] Cooper, J.W., Chen, J., Li, Y., Lee, C.S., Membrane-Based Nanoscale Proteolytic Reactor Enabling Protein Digestion, Peptide Separation, and Protein Identification Using Mass Spectrometry, Anal. Chem., 2003, 75,1067-1074.
[41] Samskog, J., Bylund, D., Jacobsson, S.P., Markides, K.E., Miniaturized on-line proteolysis-capillary liquid chromatography-mass spectrometry for peptide mapping of lactate dehydrogenase, J. Chromatogr. A., 2003, 998, 83-91.
[42] Ericsson, D., Ekstro¨m, S., Nilsson, J., Bergquist, J., Marko-Varga, G., Laurell, T., Downsizing proteolytic digestion and analysis using dispenser-aided sample handling and nanovial matrix-assisted laser/desorption ionization-target arrays, Proteomics, 2001, 1, 1072-1081.
[43] Slysz, G.W., Schriemer, D.C., On-column digestion of proteins in aqueous-organic solvents, Rapid Commun. Mass Spectrom., 2003, 17, 1044-1050.
[44] Slysz, G.W., Schrieme, D.C., Blending Protein Separation and Peptide Analysis through Real-Time Proteolytic Digestion, Anal. Chem., 2005, 77,1572-1579.
[45] Harris, W.A., Reilly, J.P., On-probe digestion of Bacterial proteins for MALDI-MS, Anal. Chem., 2002, 74, 4410-4416.
[46] Gobom, J., Nordhoff, E., Ekman, R., Roepstorff, P., Rapid micro-scale proteolysis of proteins for MALDI-MS peptide mapping using immobilized trypsin, Int. J. Mass Spectrom. Ion Processes., 1997,169,153-163.
[47] Kussmann, M., Nordhoff, E., Rahbek-Nielsen, H., Haebel, S., Rossel-Larsen, M., Jakobsen, L., Gobom, J., Mirgorodskaya, E., Kroll-Kristensen, A., Palm, L., Roepstorff, P., Matrix-assisted Laser Desorption/ Ionization Mass Spectrometry Sample Preparation Techniques Designed for Various peptide and protein analystes, J. Mass Spectrom., 1997, 32, 593-601.
[48] Dai, Y., Whittal, R. M., Li, L., Two-Layer Sample Preparation: A Method for MALDI-MS Analysis of Complex Peptide and Protein Mixtures, Anal. Chem., 1999,71,1087-1091.
[49] Ericson, C, Phung, Q. T., Horn, D. M., Peters, E. C, Fitchett, J. R., Ficarro, S. B., Salomon, A. R., Brill, L. M., Brock, A., An Automated Noncontact Deposition Interface for Liquid Chromatography Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry, Anal. Chem., 2003, 75,2309-2315.
[50] Mao, Y., Zhang, X., Comprehensive two-dimensional separation system by coupling capillary reverse-phase liquid chromatography to capillary isoelectric focusing for peptide and protein mapping with laser-induced fluorescence detection Electrophoresis, 2003, 24, 3289-3295.
[51] Yang, X., Zhang, X., Li, A., Zhu, S., Huang, Y., Comprehensive two-dimensional separations based on capillary high-performance liquid chromatography and microchip electrophoresis. Electrophoresis, 2003, 24,1451-1457.
[52] Zhang, J., Hu, H., Gao, M., Yang, P., Zhang, X., Comprehensive two-dimensional chromatography and capillary electrophoresis coupled with tandem time-of-flight mass spectrometry for high-speed proteome analysis. Electrophoresis, 2004, 25, 2374-2383
[53] Wang, Y., Zhang, J., Liu, C. L., Gu, X., Zhang, X. M., Nano-flow multidimensional liquid chromatography with electrospray ionization time-of-flight mass spectrometry for proteome analysis of hepatocellular carcinoma, Analytica Chimica Acta, 2005, 530, 227-235.
[54] Qu, Y.; Moons, L.; Vandesande, F. Determination of serotonin, catecholamins and their metabolites by direct injection of supernatants from chicken brain tissue homogenate using liquid chromatography with electrochemical detection. J. Chromatogr. B. 1997, 704, 351-358.
[55] Zhang, X., Huang, S., Single step on-column frit making for capillary high-performance liquid chromatography using sol-gel technology J. Chromatogr. A., 2001, 910,13-18
[56] Zuo, X., Echan, L., Hembach, P., Tang, H. Y., Speicher, K. D., Santoli, D., Speicher, D. W., Towards global analysis of mammalian proteomes using sample prefractionation prior to narrow pH range two-dimensional gels and using onedimensional gels for insoluble and large proteins Electrophoresi, 2001, 22,1603-1615.
[57] Zuo, X., Speicher, D. W., Comprehensive analysis of complex proteomes using microscale solution isoelectrofocusing prior to narrow pH range two-dimensional electrophoresis Proteomics, 2002, 2, 58-68.
[58] Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol., 1999,17, 994-999.
[59] Zhu, H., Pan, S., Gu, S., Bradbury, E.M., Chen, X., Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom., 2002,16, 2115-2123.
[60] Gu, S., Du, Y., Chen, J., Liu, Z., Bradbury, E.M., Hu, C.A., Chen, X., Large-Scale Quantitative Proteomic Study of PUMA-Induced Apoptosis Using Two-Dimensional Liquid Chromatography-Mass Spectrometry Coupled with Amino Acid-Coded Mass Tagging. J. Proteome Res., 2004, 3, 1191-1200.
[61] Gu, S., Liu, Z., Pan, S., Jiang, Z., Lu, H., Bradbury, E.M., Hu, C.A., Chen, X., Global Investigation of p53-induced Apoptosis Through Quantitative Proteomic Profiling Using Comparative Amino Acid-coded Tagging. Molecular & Cellular Proteomics, 2004, 3, 998-1008.
[62] Bordin, G., Raposo, F. C, Calle, B. de la, Rodriguez, A.R., Identification and quantification of major bovine milk proteins by liquid chromatography. J. Chromatogr. A, 2001, 928, 63-76.
[63] Ferreira, I.M.P.L.V.O., Cacote, H., Detection and quantification of bovine, ovine andcaprine milk percentages in protected denomination of origin cheeses by reversed-phase high-performance liquid chromatography of beta-lactoglobulins. J. Chromatogr. A., 2003, 1015,111-118.
[64] Merbel, N. C. van de, Mentink, C. J.A.L., Hendriks, G., Wolffenbuttel, B.H.R. Liquid chromatographic method for the quantitative determination of N-carboxymethyllysine in human plasma proteins. J. Chromatogr. B, 2004, 808,163-168.
[65] Bu¨nger, H.; Kaufner, L.; Pison, U., Quantitative analysis of hydrophobic pulmonary surfactant proteins by high-performance liquid chromatography with light-scattering detection. J. Chromatogr. A, 2000, 870, 363-369.
[66] Toorop, R.M., Murch, S.J., Ball, R.O., Development of a rapid and accurate method for separation and quantification of myofibrillar proteins in meat. Food Res. International, 1997, 30, 619-627.