色谱技术分离蛋白酶解和蛋白/多肽的研究进展

本综述点评了最近十年应用色谱技术解决蛋白酶解和蛋白/多肽分离的一些最新进展,涉及的研究工作大多来自中国科学家的报道.所评论的研究进展主要包括有微酶解反应器技术、先分离蛋白酶解混合肽段的bottom-up技术和先分蛋白再分离酶解后肽段的top-down技术.简而言之,微酶解反应器的新技术能够将传统的几小时的酶解时间缩短到几秒钟;而多维多模式或阵列色谱分离的新技术可以非常有效地分离蛋白质组混合物.这些新技术的进步很大程度上促进了蛋白质组学中蛋白/多肽的分离研究.     

基于非特异性蛋白酶连续酶解的蛋白质全序列测定方法

对蛋白质全序列进行测定, 有助于分析蛋白质的结构, 揭示蛋白质的生物学功能. 针对目前基于质谱的蛋白质测序流程中使用特异性蛋白酶酶解产生的肽段种类少、重叠度低、序列拼接困难等问题, 发展了一种基于非特异性蛋白酶连续酶解的蛋白质全序列测定方法. 构建了连续酶解装置, 并使用多种非特异性蛋白酶对蛋白质进行连续酶解. 利用非特异性蛋白酶酶解位点的非特异性、不同的酶解时间以及不同种类蛋白酶酶解产生肽段的互补性, 提高蛋白质酶解肽段的种类和重叠度, 并发展了蛋白质序列拼接算法对液相色谱质谱联用(LC-MS/MS)和从头测序获得的肽段序列进行拼接. 将此方法应用于牛血清白蛋白和单克隆抗体赫赛汀的全序列测定, 在不考虑亮氨酸和异亮氨酸的情况下, 对牛血清白蛋白和赫赛汀轻链的测序准确度达到100%, 赫赛汀重链的测序准确度为99.7%.     

在线微酶反应器-微柱液相色谱-电喷雾质谱用于蛋白质快速分析

采用带有环氧基的聚丙烯酸酯基质微球实现了胰蛋白酶的固定化,并制备了填充式微酶反应器.以细胞色素C为底物,考察了微酶反应器的性能.与自由溶液酶解相比,细胞色素C在微酶反应器上的酶解时间可以缩短到18s以内,速度是自由溶液酶解的2400倍.在此基础上,构建了在线微酶反应器-微柱液相色谱-电喷雾质谱联用平台,并采用4种标准蛋白混合物进行了评价.结果表明,4种蛋白均得到了较好的酶解和鉴定结果.此外,该平台还被应用于鼠肝提取蛋白的分析,共鉴定出138种蛋白,其中匹配两个或两个以上肽段的蛋白质有31个.     

非对称流场流分离-超高效液相色谱-串联四极杆飞行时间质谱用于过敏原蛋白表位筛选

应用非对称流场流分离（AF4）技术结合超高效液相色谱-四极杆飞行时间质谱（UPLC-QTOF-MS）对过敏原蛋白表位进行筛选。将选择的过敏原蛋白（虾原肌球蛋白，TM）酶解后经UPLC-QTOF-MS分析，建立蛋白质肽谱。将TM酶解后的肽段与免疫球蛋白E混合孵育30 min，孵育过程中含有抗原表位的特异性肽段与免疫球蛋白E（IgE）结合，未结合的肽段仍留在溶液中。将孵育后的溶液进行AF4分离，已结合的肽段随IgE一起由出口流出，未结合的肽段透过分离通道膜，滤出至废液。收集出口流出的组分进行UPLC-QTOF-MS分析，与蛋白质肽谱匹配，找到特异性肽段，进而检测抗原表位。本研究扩展了非对称流场流分离技术的应用，对过敏原蛋白表位的检测进行了初步探索，为过敏原蛋白表位的研究提供了一种新的研究策略。     

赖氨酸C端内切酶/胰蛋白酶顺序酶切在蛋白质组学样本制备中的评估

采用胰蛋白酶(Trypsin)单独酶切与不同酶量的赖氨酸C端内切酶(Lys-C/trypsin)顺序酶切两种方法,对293T细胞全蛋白样本进行酶解消化,系统评估Lys-C/trypsin顺序酶切与Trypsin单一酶切在蛋白质组学样本制备中的差别.实验结果表明,Lys-C/trypsin顺序酶切不仅能显著提高肽段和蛋白质的鉴定数目,同时降低遗漏K酶切位点的数目及比例,而且得到的肽段长度有利于质谱鉴定,蛋白质覆盖率明显提升.通过对酶的用量进行优化对比,最终确定了Lys-C/trypsin顺序酶切时酶的合理用量.本研究结果对提高蛋白质组学样本的制备质量以及蛋白质的序列鉴定覆盖度具有指导意义.     

亮氨酰-tRNA合成酶的限制性酶解及活性片段的研究

大肠杆菌亮氨酰-tRNA合成酶(LeuRS)经胰蛋白酶限制性酶解,被切去约6k分子量肽段,产生一96k片段。该片段具有与天然酶相同的氨基酸活化反应的动力学常数,但丧失氨酰化活性、tRNA~(Leu)结合活性等由tRNAL~(Leu)参与的一系列活性。N-末端分析表明切去的6k肽段系LeuRS C端部分,该部分是LeuRS结合tRNAL~(Leu)所必需的。本文表明LeuRS的氨基酸活化和氨酰化这两种活性是相互独立并分别处于酶分子不同的结构域。LeuRS C端部分可能是tRNA~(Leu)的结合部分。     

天花粉蛋白一级结构的修正及不同产地天花粉蛋白的研究

胰蛋白酶酶解天花粉蛋白, 用高效液相色谱分离酶解肽段, 用顺序仪测定其有关肽段的顺序。用羧肽酶A, B, Y测定了天花粉蛋白C-端和天花粉蛋白溴化氰降解肽CB1的C-端顺序, 修正了我们1985年测定的天花粉蛋白一级结构, 证明天花粉蛋白由246(7)氨基酸残基所组成, 除C-端微观不均一外, 与Collins结果一致。同时比较了芜湖产天花粉蛋白一级结构与平湖产的天花粉蛋白一级结构, 没有发现两者的一级结构有差别。     

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.     

基于四极杆-飞行时间质谱的非标记蛋白定量检测方法学研究

以四极杆飞行时间质谱检测的蛋白肽段的质谱信息为基础,开发了一种简单、准确的蛋白定性、定量检测方法,并用于牛血清白蛋白的定性、定量检测。对酶解肽段的梯度洗脱条件和流速等液相色谱条件进行了优化;进行蛋白样品的酶解及质谱检测,利用MassHunter定量软件对数据进行分析;为减少假阳性结果的出现,实验优化了数据处理软件中的设置参数,并对方法的重现性进行了考察。结果显示,重复检测的8个肽段峰面积的RSD均在3.0%以下。该方法对牛血清白蛋白的检出限为100 ng。实验发现,样品中蛋白的含量与检测到的肽段匹配率呈对数关系,并从检测到的丰度较高的8个肽段中确定可用于BSA蛋白定性检测的肽段为:HLVDEPQNLIK,定量检测的肽段为:ATEEQLK,方法的回收率为106%。该方法操作简便,检测快速,成本较低,专一性强,可用于蛋白特异性肽段的筛选及复杂生物样品中蛋白的检测。     

原子转移自由基聚合修饰银丝固定化酶反应器的制备及在蛋白质组鉴定中的应用

针对传统溶液酶解存在的酶解时间较长、酶自切物干扰以及蛋白酶不能重复使用等缺陷,通过电子转移生成催化剂的原子转移自由基聚合法修饰银丝,并以其为载体制备了一种新型的固定化酶反应器。用质谱考察了银丝固定化酶反应器(SW-Trypsin)的酶解效率、重复性和回收率。结果表明:绒毛状聚合物修饰的SW-Trypsin的酶解效率较高,酶解标准蛋白牛血清白蛋白(BSA)20 min后,肽段的氨基酸序列覆盖率可达93%,高于传统溶液酶解方法酶解16 h所得79%的覆盖率。使用该固定化酶反应器于一个月内8次酶解BSA所得的氨基酸序列覆盖率在89%到97%之间,平均覆盖率为94%,显示出良好的稳定性。另外,该固定化酶反应器酶解马心肌红蛋白(MYO)的回收率为87.67%。最后,用SW-Trypsin酶解腾冲嗜热菌全蛋白20 min,所鉴定到的氨基酸序列覆盖率和蛋白数量与同样条件下溶液酶解16 h的结果接近,且零漏切位点肽段的比例更高。加之容易分离的优点,SW-Trypsin在蛋白质组学的应用中具有良好的前景。     

C-Terminal sequencing of protein by MALDI mass spectrometry through the specific derivatization of the α-carboxyl group with 3-aminopropyltris-(2,4,6-trimethoxyphenyl)phosphonium bromide

We present here an approach to C-terminal sequencing of proteins by the procedure consisting of the following: (1) derivatization of the C-terminal α-carboxyl group with 3-aminopropyltris(2,4,6-trimethoxyphenyl)-phosphonium bromide (TMPP-propylamine) through oxazolone chemistry, (2) enzymatic proteolysis of the TMPP-derivatized protein, and (3) MALDI-MS/MS analysis of the peptide mixture, in which the C-terminal peptide incorporating the TMPP group is preferably detected. In this protocol, it is possible to choose any endoproteinase such as trypsin, GluC, and AspN for digestion so that a C-terminal peptide with length appropriate for mass spectrometric sequencing could be generated. The peptide labeled with TMPP-propylamine at the C terminus tends to exhibit y-type ions in MS/MS spectra, allowing manual sequence interpretation with the simplified fragmentation pattern. The efficacy of the method was verified with five proteins, which demonstrated that the C-terminal peptides were readily distinguishable by their peak intensity and characteristic mass signature peak in MALDI-PSD analysis.     

Identification and sequencing analysis of intact proteins via collision-induced dissociation and quadrupole time-of-flight mass spectrometry

Identifying unknown proteins has become a central focal point for proteomic and biopharmaceutical development laboratories. Our laboratory investigated using quadrupole time-of-flight mass spectrometry (Qq/TOFMS) for the analysis of intact proteins for the purpose of identifying unknowns while limiting the number of sample-handling steps between protein extraction and identification. Eight standard proteins, both unmodified and disulfide-bonded and ranging in mass from 5 to 66 kDa, were analyzed using nanoelectrospray and collision-induced dissociation to generate peptide sequence tags. An MS analysis, followed by MS/MS analyses on two to five individual protein charge states, were obtained to make an identification. Peptide sequence tags were extracted from the MS/MS data and used, in conjunction with molecular mass and source origin, to obtain protein identifications using the web-based search engine ProteinInfo (www.proteometrics.com). All of the proteins were unambiguously identified from the input data, after which, all of the major product ions were identified for structural information. In most cases, N- and/or C-terminal ions, and also stretches of consecutive product ions from the protein interior, were observed. This method was applied to the analysis and identification of an unknown detected via reversed-phase high-performance liquid chromatography.     

溴化氰裂解结合电喷雾串联质谱测定电泳分离蛋白的C端序列

C端测序是蛋白质及多肽一级结构确认的重要组成部分,也是重组蛋白药物质量控制的重要依据。建立了溴化氰裂解结合电喷雾串联质谱测定蛋白质C端序列的方法,并应用于重组人肿瘤坏死因子受体和纽兰格林的C端测序。首先根据待测蛋白序列进行溴化氰理论裂解,如果C-端肽段理论分子量在500~5000U之间,则将待测样品进行SDS-PAGE分离,考马斯亮兰染色,然后进行胶内溴化氰裂解,最后应用基质辅助激光解吸/电离飞行时间质谱(MALDI-TOF-MS)测定C-端肽段的分子量,电喷雾串联质谱对C端肽段进行测序。应用本方法分别测定了这两个蛋白质C端19个和11个氨基酸残基序列。研究结果表明:本方法灵敏、有效、实用性较强,可适用于部分重组蛋白药物的质量控制和蛋白质的结构确证,是对目前蛋白质C端测序方法的有效补充。     

De novo analysis of protein N-terminal sequence utilizing MALDI signal enhancing derivatization with Br signature

De novo analysis of protein N-terminal sequence is important for identification of N-terminal proteolytic processing such as N-terminal methionine or signal peptide removal, or for the genome annotation of uncharacterized proteins. We introduce a de novo sequencing method of protein N terminus utilizing matrix-assisted laser desorption/ionization (MALDI) signal enhancing picolinamidination with bromine isotopic tag incorporated to the N terminus. The doublet signature of bromine in the tandem mass (MS/MS) spectrum distinguished N-terminal ion series from C-terminal ion series, facilitating de novo N-terminal sequencing of protein. The dual advantage of MALDI signal enhancement by the basic picolinamidine and b-ion selection aided by Br signature is demonstrated using a variety of peptides. The N-terminal sequences of myoglobin and hemoglobin as model proteins were determined by incorporating the Br tag to the N terminus of the proteins and obtaining a series of b-ions with Br signature by MS/MS analysis after chymotryptic digestion of the tagged proteins. The N-terminal peptide was selected for MS/MS analysis from the chymotryptic digest based on the Br signature in the mass spectrum. Identification of phosphorylation site as well as N-terminal sequencing of a phosphopeptide was straightforward.     

Through the eye of an electrospray needle: mass spectrometric identification of the major peptides and proteins in the milk of the one‐humped camel (Camelus dromedarius)

The milk of the one‐humped camel (Camelus dromedarius) reportedly offers medicinal benefits, perhaps because of its unique bioactive components. Milk proteins were determined by (1) two‐dimensional gel electrophoresis and peptide mass mapping and (2) liquid chromatography–tandem mass spectrometry (LC–MS/MS) following one‐dimensional polyacrylamide gel electrophoresis. Over 200 proteins were identified: some known camel proteins including heavy‐chain immunoglobulins and others exhibiting regions of exact homology with proteins from other species. Indigenous peptides were also identified following isolation and concentration by two strategies: (1) gel‐eluted liquid fraction entrapment electrophoresis and (2) small‐scale electrophoretic separation. Extracts were analyzed by LC–MS/MS and peptides identified by matching strategies, by de novo sequencing and by applying a sequence tag tool requiring similarity to the proposed sequence, but not an exact match. A plethora of protein cleavage products including some novel peptides were characterized. These studies demonstrate that camel milk is a rich source of peptides, some of which may serve as nutraceuticals. Copyright © 2013 John Wiley & Sons, Ltd.     

A method combining SPITC and 18O labeling for simultaneous protein identification and relative quantification

The relative quantification and identification of proteins by matrix‐assisted laser desorption ionization time‐of‐flight MS is very important in /MS is very important in protein research and is usually conducted separately. Chemical N‐terminal derivatization with 4‐sulphophenyl isothiocyanate facilitates de novo sequencing analysis and accurate protein identification, while ¹⁸O labeling is simple, specific and widely applicable among the isotopic labeling methods used for relative quantification. In the present study, a method combining 4‐sulphophenyl isothiocyanate derivatization with ¹⁸O isotopic labeling was established to identify and quantify proteins simultaneously in one experiment. Reaction conditions were first optimized using a standard peptide (fibrin peptide) and tryptic peptides from the model protein (bovine serum albumin). Under the optimized conditions, these two independent labeling steps show good compatibility, and the linear relativity of quantification within the ten times dynamic range was stable as revealed by correlation coefficient analysis (R² value = 0.998); moreover, precursor peaks in MS/MS spectrum could provide accurate quantitative information, which is usually acquired from MS spectrum, enabling protein identification and quantification in a single MS/MS spectrum. Next, this method was applied to native peptides isolated from spider venoms. As expected, the de novo sequencing results of each peptide matched with the known sequence precisely, and the measured quantitative ratio of each peptide corresponded well with the theoretical ratio. Finally, complex protein mixtures of spider venoms from male and female species with unknown genome information were analyzed. Differentially expressed proteins were successfully identified, and their quantitative information was also accessed. Taken together, this protein identification and quantification method is simple, reliable and efficient, which has a good potential in the exploration of peptides/proteins from species with unknown genome. Copyright © 2014 John Wiley & Sons, Ltd.     

CHASE, a charge-assisted sequencing algorithm for automated homology-based protein identifications with matrix-assisted laser desorption/ionization time-of-flight post-source decay fragmentation data

We describe CHASE, a novel algorithm for automated de novo sequencing based on the mass spectrometric (MS) fragmentation analysis of tryptic peptides. This algorithm is used for protein identification from sequence similarity criteria and consists of four steps: (1) derivatization of tryptic peptides at the N-terminus with a negatively charged reagent; (2) post-source decay (PSD) fragmentation analysis of peptides; (3) interpretation of the mass peaks with the CHASE algorithm and reconstruction of the amino acid sequence; (4) transfer of these data to software for protein identifications based on sequence homology (Basic Local Alignment Search Tool, BLAST). This procedure deduced the correct amino acid sequence of tryptic peptide samples and also was able to deduce the correct sequence from difficult mass patterns and identify the amino acid sequence. This allows complete automation of the process starting from MS fragmentation of complex peptide mixtures at low concentration (e.g. from silver-stained gel bands) to identification of the protein. We also show that if PSD data are collected in a single spectrum (instead of the segmented mode offered by conventional matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instrumentation), the complete workflow from MS-PSD data acquisition to similarity-based identification can be completely automated. This strategy may be applied to proteomic studies for protein identification based on automated de novo sequencing instead of MS or tandem MS patterns. We describe the Charge Assisted Sequencing Engine (CHASE) algorithm, the working protocol, the performance of the algorithm on spectra from MALDI-TOFMS and the data comparison between a TOF and a TOF-TOF instrument.     

Cleavable hydrophilic linker for one-bead-one-compound sequencing of oligomer libraries by tandem mass spectrometry

We have developed a method for the rapid and unambiguous identification of sequences of hit compounds from one-bead-one-compound combinatorial libraries of peptide and peptoid ligands. The approach uses a cleavable linker that is hydrophilic to help reduce nonspecific binding to biological samples and allows for the attachment of a halogen tag, which greatly facilitates post-screening sequencing by tandem mass spectrometry (MS/MS). The linker is based on a tartaric acid unit, which, upon cleavage from resin, generates a C-terminal aldehyde. This aldehyde can then be derivatized with a bromine-containing amino-oxy compound that serves as an isotope tag for subsequent MS/MS analysis of y-ion fragments. We have applied this linker and method to the syntheses of a number of peptoids that vary in sequence and length and have also demonstrated single-bead sequencing of a peptoid pentamer. The linker is also shown to have very low levels of nonspecific binding to proteins.     

微柱高效液相色谱-质谱/质谱快速鉴定混合蛋白质新方法

发展了一种混合蛋白质快速鉴定的新方法.将几种蛋白质的混合物于热变性后直接在溶液中酶解,利用微柱高效液相色谱-离子阱串级质谱进行肽谱/氨基酸序列分析,并结合Mascot数据库搜索处理功能,实现了混合蛋白质快速准确的鉴定.     

Studies on Fragmentation Pathways of N-Ethoxy （phenyl） phosphoryl Amino Acids by Electrospray Ionization Tandem Mass Spectrometry

IntroductionPhosphorylation often acts as a molecular switchcontrolling the protein activity in different pathways asin metabolism,signal transduction,cell division,andso on.Therefore,N-phosphoryl amino acids play aspecial and important role in biological…