反相高效液相色谱双梯度洗脱分离肽混合物及质谱分析

复杂肽段混合物的有效分离是高覆盖率地鉴定蛋白质混合物的前提。“鸟枪法”(Shotgun)蛋白质组学研究策略通常采用蛋白酶切、二维液相色谱-串联质谱分析肽段混合物从而鉴定蛋白质,其中高效率地分离肽段混合物是关键步骤之一。本文通过pH梯度结合有机溶剂梯度的反相高效液相色谱(RP-HPLC)进行一维液相色谱分离,按等时间间隔收集馏分并将一个梯度的前段的一个馏分与后段一个馏分混合,然后进行纳升级液相色谱-质谱联用(nanoRPLC-MS/MS)分析。将该方法应用于酵母蛋白质的分离和鉴定,实验结果为: 与常规的强阳离子色谱-反相液相色谱-质谱分离鉴定方法相比,采用pH梯度结合有机相梯度的RP-HPLC-RPLC-MS分离鉴定方法多鉴定到567个酵母蛋白质(簇,含有3035个唯一肽段);其中鉴定到肽段的pI分布范围为3.42～12.01,相对分子质量范围为587.67～3499.79;蛋白质的pI分布范围为3.82～12.19,相对分子质量范围为3446.55～432905。该结果表明这种方法在复杂体系蛋白质组分离鉴定中具有明显的优势,在蛋白质组学研究中有较好的应用前景。     

新型全二维微柱液相色谱分离平台的构建

采用自动进样器和一套二元梯度泵构建了以阳离子交换色谱-反相色谱(SCX-RPLC)为分离模式的新型全二维微柱液相色谱分离平台.在第一维分离中,通过自动进样器将不同浓度的盐溶液以台阶梯度输送至SCX柱上,实现肽段的分级洗脱.洗脱下的肽段经C8预柱富集、除盐后,进入第二维C18 RPLC柱上,通过线性梯度实现进一步的分离.采用该平台分离了5种标准蛋白的酶解产物,系统峰容量可达1 467.结果表明,该平台可以自动完成进样、除盐、分离及检测.     

亲水作用-反相二维液相色谱串联质谱法鉴定水稻蛋白质

建立了亲水作用-反相二维液相色谱串联质谱分析水稻叶片蛋白质组学的方法。利用标准肽段系统分析了液相色谱流动相酸碱度对二维亲水作用-反相色谱系统正交性的影响。结果表明,第一维亲水作用色谱在碱性(pH 9.3)和第二维反相色谱在酸性(pH 3.3)的条件下,正交性最佳(R~2=0.34113)。在此基础上,结合馏分收集技术进一步评价了本测试系统在水稻叶片蛋白质分析中的正交性。结果表明,在所有馏分收集组分中,鉴定次数小于2次的水稻叶片肽段占总肽段数目的 50%以上,且一维液相色谱馏分收集的肽段在第二维色谱及质谱分离分析中,可以较好地分布在不同时间段的洗脱窗口,表明本研究建立的亲水作用-反相二维液相色谱串联质谱结合馏分收集技术在复杂水稻叶片蛋白质分离鉴定中可提供良好的的分离正交性。结合水稻蛋白质数据库检索,共鉴定出207345个肽段,归属于2930个蛋白质簇。     

毛细管整体柱在线二维分离系统应用于人体软骨的蛋白质组分析

将已建立的 7 cm 柱长的磷酸基团强阳离子交换富集整体柱与85 cm柱长的C12烷基反相整体柱结合的在线二维分离平台应用于软骨提取蛋白的蛋白质组分析。对20 μg软骨提取蛋白的酶解产物进行14个盐梯度的分级,然后对14个馏分进行反相色谱梯度分离及串联质谱鉴定,成功地鉴定得到了7434个独立肽段对应的1901个非冗余蛋白质。对所鉴定到的蛋白质进行定位分类,结果表明鉴定到的大部分蛋白质是来自于软骨细胞内部的低丰度蛋白质,这对于许多关节类疾病的研究有重要意义。     

液相色谱-质谱法比较分析正常人与胃癌患者的胃组织蛋白质

通过蛋白质组学技术筛选胃癌相关标志物是目前胃癌研究的热点,也是早期诊断的关键。针对组织蛋白质提取物非常复杂的特点,并根据疏水性的差异,采用反相液相色谱对正常及癌症组织提取蛋白质进行分离。通过比较正常及癌症组织提取蛋白质的谱图差异,收集并酶解差异最大的保留时间为45～47 min的馏分,采用液相色谱-多级质谱联用(LC-MS/MS)鉴定其酶解产物。鉴定结果显示,正常及癌症组织中的共有蛋白质为9个,正常组织中有6个特异蛋白质,而癌症组织中有17个特异蛋白质。通过进一步分析,筛选出胃癌组织中含有的丰度较高的两个蛋白质。应用生物信息学方法分析这些蛋白质,能为将来的药物靶点、药物作用通路研究提供更多的信息。     

离线pH梯度-强阳离子交换色谱法分离肽段混合物

复杂肽段混合物的有效分离是高覆盖率地鉴定蛋白质混合物的前提。Shotgun蛋白质组学研究通常采用二维液相色谱(强阳离子交换色谱-反相色谱)分离后接串联质谱检测的方法。但由于离子交换色谱体系中含有高浓度的盐,使得在线分析的难度较大;而在离线分析时,也常因需要对高盐组分进行脱盐处理而易引起样品损失。因此,该文尝试用pH梯度替代盐梯度,实现pH梯度-强阳离子交换色谱方法应用于复杂肽段混合物的分离。通过对缓冲体系pH值的计算,优化了乙酸-乙酸铵体系线性pH梯度配合盐梯度的离子交换色谱方法,以及柠檬酸-氨水体系线性pH梯度的离子交换色谱方法。将这两种方法应用于牛血清白蛋白酶切产物的分离取得了与常规强阳离子交换色谱相似的分离效果。乙酸-乙酸铵体系采用的是低浓度的可挥发性铵盐,采用真空冻干的方法可以有效除盐,基质辅助激光解吸质谱靶上自然挥发也可以达到较好的脱盐效果,简化了常规方法繁琐费时的脱盐步骤及避免了由此造成的样品损失。柠檬酸-氨水体系采用pH梯度洗脱替代盐梯度洗脱,大大降低了体系中的盐浓度。这两种方法在复杂体系蛋白质组研究的样本预分离中具有较好的应用前景。     

鼠肝蛋白质组的纳升级多维液相色谱分离

搭建了一个纳升级的二维液相色谱分离平台(nano-2D-LC),该平台可以自动完成进样、除盐、分离及鉴定。以离子交换色谱(SCX)为第一维,反相液相色谱(RPLC)为第二维,对鼠肝组织的蛋白质组进行了研究。SCX采用阶梯式洗脱,RPLC运用线性梯度洗脱,以200 nL/min的速度进行分离,峰容量可达620。     

基于不同提取方法的水稻叶片蛋白质组的二维液相色谱分离及高分辨质谱分析

建立了酚法提取-二维液相色谱分离-高分辨质谱分析水稻叶片蛋白质组的方法。水稻叶片蛋白质经过酚法提取,酶解肽段脱盐后用离线反相-反相二维液相色谱分离,然后用线性离子阱/静电场轨道阱组合式高分辨质谱分析,共鉴定到2712种蛋白质。比较了液相色谱分离系统（一维液相色谱与二维液相色谱）和水稻叶片蛋白质提取方法（酚法、十二烷基硫酸钠法（SDS法）和三氯乙酸/丙酮法（TCA/丙酮法））对鉴定蛋白质数量的影响,结果表明：在二维液相色谱条件下,酚法、SDS法和TCA/丙酮法鉴定到的蛋白质数目为2712、2415和1914,分别是一维液相色谱条件下鉴定到的蛋白质数目的2.7、2.5和1.9倍。二维液相色谱条件下,酚法鉴定到的蛋白质数目比SDS法和TCA/丙酮法分别多297和798。与SDS法和TCA/丙酮法相比,酚法不但鉴定到的蛋白质数量多,而且能够鉴定到一些极端蛋白质,如酸性、碱性及高等电点的蛋白质。此外,对二维液相色谱条件下3种蛋白质提取方法提取到的蛋白质进行生物学功能分类,发现3种方法鉴定到的蛋白质的功能存在互补性,但酚法鉴定到的蛋白质功能种类最多。该法为水稻蛋白质组学研究提供了技术支撑,同时也为其他作物的蛋白质组学研究技术提供重要的借鉴。     

毛细管反相液相色谱-串联质谱用于肽的鉴定和相对定量分析

建立了一种基于毛细管反相液相色谱-串联质谱联用技术和质谱峰强度数据处理的肽段鉴定和相对定量分析方法。该方法无需对样品中的肽进行化学标记,在对样品进行反相色谱分离和串联质谱分析后,将二级质谱扫描数据进行蛋白质数据库搜索,获得所鉴定肽段的序列、保留时间、质荷比、带电荷数等定性信息;再以此为定位依据,在全扫描质谱数据中提取该肽段对应的离子峰并以该离子峰的峰强度作为定量信息,从而实现对不同样品中的共有肽段进行差异比较分析。以标准蛋白酶解混合肽段为实验对象,以肽段相对强度的相对标准偏差为指标,考察了该方法用于肽段相对定量分析的重现性、检测动态范围以及浓度标准曲线等,为将该方法用于生物样品中内源性肽的差异分析奠定了基础。     

反相高效液相色谱法测定蟾酥中的3种蟾毒内酯

建立了一种基于毛细管反相液相色谱-串联质谱联用技术和质谱峰强度数据处理的肽段鉴定和相对定量分析方法。该方法无需对样品中的肽进行化学标记,在对样品进行反相色谱分离和串联质谱分析后,将二级质谱扫描数据进行蛋白质数据库搜索,获得所鉴定肽段的序列、保留时间、质荷比、带电荷数等定性信息;再以此为定位依据,在全扫描质谱数据中提取该肽段对应的离子峰并以该离子峰的峰强度作为定量信息,从而实现对不同样品中的共有肽段进行差异比较分析。以标准蛋白酶解混合肽段为实验对象,以肽段相对强度的相对标准偏差为指标,考察了该方法用于肽段相对定量分析的重现性、检测动态范围以及浓度标准曲线等,为将该方法用于生物样品中内源性肽的差异分析奠定了基础。。     

Development of an online two-dimensional nano-scale liquid chromatography/mass spectrometry method for improved chromatographic performance and hydrophobic peptide recovery

An online two-dimensional (2D) strong cation-exchange (SCX)/reversed-phase (RP) nano-scale liquid chromatography/mass spectrometry (nanoLC/MS) method was developed for improved separation and hydrophobic peptide recovery. Sharper and more symmetric RP peaks were observed with the use of a "band re-focusing method", in which an analytical RP column with more hydrophobicity than the RP trap column was used in the system. To recover hydrophobic peptides still unreleased from the SCX column after a conventional salt step gradient due to hydrophobic interaction, a RP step gradient from 10% to 30% acetonitrile (ACN) was applied to the SCX column in the presence of a high salt concentration following the salt gradient. There were 301 unique hydrophobic E. coli peptides identified from the RP fractions. These peptides, which were 19% of all E. coli peptides identified from a 2D run, would not have been identified without the application of the RP gradient to the SCX column.     

Dual-purpose sample trap for on-line strong cation-exchange chromatography/reversed-phase liquid chromatography/tandem mass spectrometry for shotgun proteomics. Application to the human Jurkat T-cell proteome

A dual-purpose sample-trapping column is introduced for the capacity enhancement of proteome analysis in on-line two-dimensional nanoflow liquid chromatography (strong cation-exchange chromatography followed by reversed-phase liquid chromatography) and tandem mass spectrometry. A home-made dual trap is prepared by sequentially packing C18 reversed-phase (RP) particles and SCX resin in a silica capillary tubing (1.5 cm x 200 microm I.D. for SCX, 0.7 cm x 200 microm for RP) ended with a home-made frit and is connected to a nanoflow column having a pulled tip treated with an end frit. Without having a separate fraction collection and concentration process, digested peptide mixtures were loaded directly in the SCX part of the dual trap, and the SCX separation of peptides was performed with a salt step elution initiated by injecting only 8 microL of NH4HCO3 solution from the autosampler to the dual trap. The fractionated peptides at each salt step were directly transferred to the RP trap packed right next to the SCX part for desalting, and a nanoflow LC-MS-MS run was followed. During the sample loading-SCX fractionation-desalting, flow direction was set to bypass the analytical column to prevent contamination. The entire 2D-LC separation and MS-MS analysis were automated. Evaluation of the technique was made with an injection of 15 microg peptide mixtures from human Jurkat T-cell proteome, and the total seven salt step cycles followed by each RPLC run resulted in an identification of 681 proteins.     

On-line strong cation exchange micro-HPLC-ESI-MS/MS for protein identification and process optimization

We have developed an on-line strong cation exchange (SCX)-ESI-MS/MS platform for the rapid identification of proteins contained in mixtures. This platform consists of a SCX precolumn followed by a nanoflow SCX column on-line with an electrospray ion trap mass spectrometer. We also used this platform to study the dynamics of peptide separation/extraction by SCX, in particular to understand the parameters affecting the performance of SCX in multidimensional chromatography. For example, we have demonstrated that the buffer typically used for tryptic digestion of protein mixtures can have a detrimental effect on the chromatographic behaviour of peptides during SCX separations, thereby affecting certain peptide quantitation approaches that rely on reproducible peptide fractionation. We have also demonstrated that band broadening results when a step (discontinuous) gradient approach is used to displace peptides from the SCX precolumn, reducing the separation power of SCX in multidimensional chromatography. In contrast, excellent chromatographic peak shapes are observed when a defined (continuous) gradient is used. Finally, using a tryptic digest of a protein extract derived from human K562 cells, we observed that larger molecular weight peptides are identified using this on-line SCX approach compared to the more conventional reverse phase (RP) LC/MS approach. Both methods used in tandem complement each other and can lead to a greater number of peptide identifications from a given sample.     

On-line parallel reversed phase two-dimensional liquid chromatography for high-throughput analysis of complex proteomic samples

A comprehensive two-dimensional liquid chromatographic system (2D SCX/RP) is con- structed with a 10-port-2-way valve using strong cation exchange chromatography (Hypersil SCX, 100 mm×4.6 mm I.D.) followed by reversed phase chromatography (Hypersil BDS C18, 15 mm×4.6 mm I.D.) to separate the complex peptides from globin peptic hydrolysate. After the sample was loaded on the SCX column, the phosphate buffer (pH 4.0) was used to elute the peptides. Then, elutes flowed through the interface and the peptides focused on the head of the trapping columns (Hypersil BDS C18, 15 mm×4.6 mm I.D.) but salt passed into the waste. After the valve was switched, the samples were flushed with a backward flow into the RP analytical column. The peptides on the SCX were eluted with 12 discontinuous steps linearly increasing salt concentrations. The peptides enriched on the trapping column were desalted and separated by the RP columns. The resolution and the resolved peaks of the 2D SCX/RP system were greatly increased and the total peak capacity reached as high as 2280.     

多维液相色谱-质谱用于酶解猪血蛋白中活性肽的研究

以强阳离子交换柱（SCX）为一维色谱柱，反相柱（RP）为二维色谱柱，采用在线捕集接口形式，通过10通阀连接一、二维色谱柱，构建了二维液相色谱分离系统。将该系统用于酶解猪血蛋白中对血管紧缩素Ⅰ转移酶（ACE）具有活性抑制作用的肽进行分离、鉴定，共检测出104个组分。收集一维馏分，离线注入LC—MS，鉴定出其中含有SAL、DKF、ESF、STVL及FESF5个小肽。     

Separation of peptides on mixed mode of reversed-phase and ion-exchange capillary electrochromatography with a monolithic column

The mixed mode of reversed phase (RP) and strong cation-exchange (SCX) capillary electrochromatography (CEC) based on a monolithic capillary column has been developed. The capillary monolithic column was prepared by in situ copolymerization of 2-(sulfooxy)ethyl methacrylate (SEMA) and ethylene dimethacrylate (EDMA) in the presence of porogens. The sulfate group provided by the monomer SEMA on the monolithic bed is used for the generation of the electroosmotic flow (EOF) from the anode to the cathode, but at the same time serves as a SCX stationary phase. A mixed-mode (RP/SCX) mechanism for separation of peptides was observed in the monolithic column, comprising hydrophobic and electrostatic interaction as well as electrophoretic migration at a low pH value of mobile phase. A column efficiency of more than 280,000 plates/m for the unretained compound has been obtained on the prepared monoliths. The relative standard deviations observed for t(0) and retention factors of peptides were about 0.32% and less than 0.71% for ten consecutive runs, respectively. Effects of mobile phase compositions on the EOF of the monolithic column and on the separation of peptides were investigated. The selectivity on separation of peptides in the monolithic capillary column could be easily manipulated by varying the mobile phase composition.     

Two-dimensional capillary liquid chromatography: pH gradient ion exchange and reversed phase chromatography for rapid separation of proteins

In the present work, an orthogonal two-dimensional (2D) capillary liquid chromatography (LC) method for fractionation and separation of proteins using wide range pH gradient ion exchange chromatography (IEC) in the first dimension and reversed phase (RP) in the second dimension, is demonstrated. In the first dimension a strong anion exchange (SAX) column subjected to a wide range (10.5-3.5) descending pH gradient was employed, while in the second dimension, a large pore (4,000 A) polystyrene-divinylbenzene (PS-DVB) RP analytical column was used for separation of the protein pH-fractions from the first dimension. The separation power of the off-line 2D method was demonstrated by fractionation and separation of human plasma proteins. Seventeen pH-fractions were manually collected and immediately separated in the second dimension using a column switching capillary RP-LC system. Totally, more than 200 protein peaks were observed in the RP chromatograms of the pH-fractions. On-line 2D analysis was performed for fractionation and separation of ten standard proteins. Two pH-fractions (basic and acidic) from the first dimension were trapped on PS-DVB RP trap columns prior to back-flushed elution onto the analytical RP column for fast separation of the proteins with UV/MS detection.     

强阳离子交换毛细管液相色谱-反相加压毛细管电色谱二维系统的构建及其在中药黄柏提取物分离中的应用

加压毛细管电色谱(pCEC)具有电泳和液相色谱的双重分离机理,其柱效高、选择性强、分辨率高和分离速度快并可进行梯度洗脱。我们在此基础上加入离子交换色谱模式,构建了强阳离子交换-反相加压毛细管液相色谱(micro strong cation exchange liquid chromatography/reversed phase pressurized capillary electrochromatography, μ-SCXLC/RP-pCEC)二维系统,并对中药黄柏的提取物进行了优化分离。第一维μ-SCXLC采用线性盐梯度分离,样品被切割成11个馏分洗脱收集后进入第二维,第二维脱盐后,采用RP-pCEC进行分离分析,梯度洗脱。以中药黄柏提取物为样品,此二维系统的分辨率和峰容量都较一维系统有很大提高,理论峰容量可达900左右,证明构建的二维体系非常适合复杂样品的分离分析。     

Two-dimensional strong cation exchange/porous layer open tubular/mass spectrometry for ultratrace proteomic analysis using a 10 microm id poly(styrene- divinylbenzene) porous layer open tubular column with an on-line triphasic trapping column

This study expands the capabilities for ultratrace proteomic analysis of our previous work by incorporating on-line sample desalting using a triphasic (RP/strong cation exchange (SCX)/micro-SPE) trapping column connected to a 3.2 m x 10 microm id poly(styrene-divinylbenzene) (PS-DVB) porous layer open tubular (PLOT) column. To minimize extra sample handling steps, C18 RP packing was incorporated in the capillary tubing upstream of the SCX column for the on-line desalting. For the micro-SPE column, a 50 microm id PS-DVB monolithic column was positioned downstream of the SCX column. High-performance separation was achieved on the PLOT column at a mobile phase flow rate of 20 nL/min. The sensitivity and high resolution capability of the new multidimensional platform was evaluated using an in-gel tryptic digested sample of a cervical cancer (SiHa) cell line. For the injected amount of 1200 cells ( approximately 500 ng), over 2700 peptides covering greater than 850 unique proteins were identified from the triphasic SCX/PLOT/MS analysis of a single SDS gel section (>40 kDa). The 2-D LC/MS platform demonstrated good separation performance, such that more than 85% of the identified peptides were detected from only one salt fraction. In a triplicate analysis of the above >40 kDa gel section, 4497 peptides and 1209 unique proteins were identified when applying stringent filtering criteria, with a false-positive rate of 2.4%. When all three SDS-PAGE gel sections of the lysed SiHa cells were analyzed, 5047 peptides and 1857 unique proteins (false-positive rate 1.8%), including cancer-related proteins such as MAP kinases, were identified.