串级质谱应用于蛋白质科学研究的实例介绍

串级质谱（MS/MS）分析是近年来迅猛发展的仪器分析技术,对于化学相关学科与其他交叉领域都起到了极大的推动作用。在使用计算机辅助解析后,常常需要进一步进行图谱指认,而这部分内容常常被化学教学所忽略。从串级质谱的原理出发,详细分析了肽段在二级质谱中可能的断裂模式与结构特性,并进一步以模型蛋白为例详细分析了串级质谱的图谱指认和峰的归属的基本原理与实用性方法,以期对教学与科研有助。     

胶内差异双向电泳-电喷雾串联质谱筛选UVB损伤皮肤细胞潜在的蛋白质靶标

联用胶内差异双向电泳(2D-DIGE)和高效液相色谱-电喷雾串联质谱(HPLC-nESI MS/MS)鉴定人角质形成细胞HaCaT应答中波紫外线(UVB)损伤的差异表达蛋白,筛选UVB影响皮肤细胞正常生理功能潜在的靶标蛋白.结果表明:UVB辐射明显影响HaCaT细胞的蛋白质表达谱,DeCyder软件在每块DIGE凝胶上...     

液相等电聚焦结合双向凝胶电泳分离碱性蛋白

在蛋白组学研究中, 经典的双向凝胶电泳法(2-DE)对碱性蛋白及低丰度蛋白的分离存在技术障碍, 但预分离技术的应用可弥补其缺陷. 液相等电聚焦可有效地分离富集复杂蛋白样品. 碱性胶条用于2-DE可极大地提高蛋白上样量和凝胶分辨率. 将上述两种技术相结合用于碱性蛋白质和低丰度蛋白质的分离鉴定, 可使碱端区域双向凝胶图谱质量显著提高, 蛋白点更清晰且点数增多, 质谱鉴定确信度提高, 碱性蛋白和低丰度蛋白质谱鉴定成功率提高, 对于蛋白组学研究具有一定的意义.     

蛋白质组学技术筛选与鉴定在甲基对硫磷胁迫下牙鲆脑组织表达的差异蛋白质

以甲基对硫磷(MP)为有机磷农药污染源,采用蛋白质组学技术分离及鉴定在甲基对硫磷胁迫下,牙鲆(Paralichthys olivaceus)脑组织表达的差异蛋白质,从中筛选出潜在的适合于监测甲基对硫磷污染程度的蛋白指示物。实验结果表明:在甲基对硫磷胁迫下,牙鲆脑组织表达出17个差异蛋白质,经肽质量指纹(PMF)图谱技术鉴定后,发现其中部分差异蛋白质为热休克蛋白、细胞色素P450和谷胱甘肽S-转移酶,均是与受甲基对硫磷胁迫有关的蛋白质。     

2D-DIGE-HPLC-nESIMS/MS对2,4-二硝基苯磺酸损伤HaCaT细胞差异蛋白质的鉴定

采用Cy2、Cy3和Cy5荧光染料标记蛋白,建立了人角质形成细胞HaCaT受2,4-二硝基苯磺酸(DNBS)刺激前后的双向胶内差异凝胶电泳(2D-DIGE)图谱,每组平行样本数为3。凝胶采用蛋白荧光染料Deep Purple进行后染色(Post-stain)。DeCyder定量分析软件在每块凝胶上平均检测到1 200个以上蛋白斑点,每块胶上都匹配得到的相同蛋白质斑点有846个。其中有7个斑点丰度变化在50%以上,统计学意义显著(P值小于0.05)。利用高效液相色谱-电喷雾串联质谱(HPLC-nESI MS/MS)成功鉴定5个表达上调的斑点分别为X染色体开放阅读框26(Cxorf26)、人辅分子伴侣23(PTGES3)、钙调蛋白(CALM3)、肌球蛋白轻链6(MYL6)和断裂点丛集区蛋白1(BANF1);2个表达下调蛋白斑点被鉴定为转录延伸因子B肽链2(TCEB2)和核糖体蛋白L23(RPL23)。除MYL6被报道与皮肤疾病相关外,其它蛋白与皮肤病变的关系有待研究。该研究得到的7个差异表达蛋白为DNBS类化学致癌物职业接触者皮肤病变研究提供了有价值的线索。     

Improved in-gel approaches to generate peptide maps of integral membrane proteins with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

This paper reports studies of in-gel digestion procedures to generate MALDI-MS peptide maps of integral membrane proteins. The methods were developed for the membrane domain of the mannitol permease of E. coli. In-gel digestion of this domain with trypsin, followed by extraction of the peptides from the gel, yields only 44% sequence coverage. Since lysines and arginines are seldomly found in the membrane-spanning regions, complete tryptic cleavage will generate large hydrophobic fragments, many of which are poorly soluble and most likely contribute to the low sequence coverage. Addition of the detergent octyl-beta-glucopyranoside (OBG), at 0.1% concentration, to the extraction solvent increases the total number of peptides detected to at least 85% of the total protein sequence. OBG facilitates the recovery of hydrophobic peptides when they are SpeedVac dried during the extraction procedure. Many of the newly recovered peptides are partial cleavage products. This seems to be advantageous since it generates hydrophobic fragments with a hydrophilic solubilizing part. In-gel CNBr cleavage resulted in 5-10-fold more intense spectra, 83% sequence coverage, fully cleaved fragments and no effect of OBG. In contrast to tryptic cleavage sites, the CNBr cleavage sites are found in transmembrane segments; cleavage at these sites generates smaller hydrophobic fragments, which are more soluble and do not need OBG. With the results of both cleavages, a complete sequence coverage of the membrane domain of the mannitol permease of E. coli is obtained without the necessity of using HPLC separation. The protocols were applied to two other integral membrane proteins, which confirmed the general applicability of CNBr cleavage and the observed effects of OBG in peptide recovery after tryptic digestion.     

Micro-high-performance liquid chromatography platform for the depletion of high-abundance proteins and subsequent on-line concentration/capturing of medium and low-abundance proteins from serum. Application to profiling of protein expression in healthy and osteoarthritis sera by 2-D gel electrophoresis

In this investigation, an integrated microcolumn-based fluidic platform for the simultaneous depletion of high-abundance proteins and the subsequent on-line concentration/capturing of medium- and low-abundance proteins from human serum has been introduced. The platform consists of on-line coupling of tandem affinity micorcolumns to an RP microcolumn to achieve first the depletion of high-abundance proteins by the tandem affinity microcolumns followed by the concentration and capturing of medium- and low-abundance proteins by the RP microcolumn. The tandem affinity microcolumns are based on macroporous monoliths characterized by their relatively high permeability in pressure-driven flow while the RP microcolumn is packed with polymeric particles with an average particle diameter of 20 microm giving rise to a very little back pressure, thus allowing fast flow velocity across the coupled columns format and consequently short processing time of serum samples prior to analysis by 2-DE. The microcolumn-based fluidic platform was applied to serum samples from osteoarthritis (OA) donors before and after soy protein (SP) supplementation, and from healthy donors, and the resulting depleted serum samples from high-abundance proteins were profiled for protein expression by 2-DE. In general, the protein expression was lower in serum of the same OA patient after soy treatment than before soy treatment. Several proteins were down-regulated after soy treatment with transthyretin being the most affected by the SP supplementation. In addition, with respect to serum from healthy donors, the sera from OA patients showed difference in proteins expression.     

Ultrathin-layer sodium dodecyl sulfate disc electrophoresis of proteins in the range from 10 to 220 kDa in homogeneous,low-concentrated polyacrylamide gels

This study describes an ultrathin-layer sodium dodecyl sulfate (SDS) disc electrophoresis in polyacrylamide gels of a thickness of only 150 microm. By use of 2-amino-2-methyl-1,3-propanediol/glycine instead of traditional Tris/HCl buffer in the resolving phase of the gel, proteins with a wide range of molecular sizes (10 kDa to over 220 kDa) are separated in unusually low-concentrated gels (4%T, 3.3%C). 2-Amino-2-methyl-1,3-propanediol in the resolving part of the gel contributes to stabilization of the pH value at 8.8, while glycine improves destacking as well as separation of small proteins from the bulk of stacked SDS. This method combines both the advantages of conventional slab-gel electrophoresis and capillary gel electrophoresis. It is easy to apply and well suited for all further miniaturization attempts.     

Development of an SDS‐gel electrophoresis method on SU‐8 microchips for protein separation with LIF detection: Application to the analysis of whey proteins

This work describes the development of an SDS‐gel electrophoresis method for the analysis of major whey proteins (α‐lactalbumin, β‐lactoglobulin, and BSA) carried out in SU‐8 microchips. The method uses a low‐viscosity solution of dextran as a sieving polymer. A commercial coating agent (EOTrol LN) was added to the separation buffer to control the EOF of the chips. The potential of this coating agent to prevent protein adsorption on the walls of the SU‐8 channels was also evaluated. Additionally, the fluorescence background of the SU‐8 material was studied to improve the sensitivity of the method. By selecting an excitation wavelength of 532 nm at which the background fluorescence remains low and by replacing the mercury arc lamp by a laser in the detection system, an LOD in the nanomolar range was achieved for proteins derivatized with the fluorogenic reagent Chromeo P540. Finally, the method was applied to the analysis of milk samples, demonstrating the potential of SU‐8 microchips for the analysis of proteins in complex food samples.     

Use of MDLC-DIGE and LC-MS/MS to identify serum biomarkers for complete remission in patients with acute myeloid leukemia

The response criteria for complete remission (CR) in acute myeloid leukemia (AML) are currently based on morphology and blood cell counts. However, these criteria are insufficient to establish a diagnosis in cases with poor quality bone marrow (BM) samples demonstrating a loss of cellular morphology. We investigated whether the sera of patients contained biomarkers that indicate disease response status. First, we performed multidimensional liquid chromatography-differential gel electrophoresis (MDLC-DIGE) to generate protein profiles of two pooled, paired serum samples from patients who had achieved CR; one collected at diagnosis (PreCR) and the other collected after chemotherapy (CR). Then, with the biomarker candidates found, ELISA was carried out for individual PreCR and CR samples, and for other verification sets including nonremission (NR) patients and normal samples. We selected two proteins, complement factor H (CFH) and apolipoprotein H (ApoH), with dye (Cy) ratios showing greater than 2.0-fold differences between the pooled samples. ELISA showed that CFH and ApoH are useful for distinguishing between the recovered (CR and normal) and nonrecovered (PreCR, PreNR, and NR) states in AML (p <0.001). We successfully applied a protein profiling technology of MDLC-DIGE and LC-MS/MS to discover two biomarkers for CR which needs further validation for a clinical setting.     

What theoretical and/or chemical significance is to be attached to the magnitude of an activation energy determined for a solid-state decomposition?

This critical survey argues that the theory, conventionally used to interpret kinetic data measured for thermal reactions of initially solid reactants, is not always suitable for elucidating reaction chemistry and mechanisms or for identifying reactivity controls. Studies of solid-state decompositions published before the 1960s usually portrayed the reaction rate as determined by Arrhenius type models closely related to those formulated for homogeneous rate processes, though scientific justifications for these parallels remained incompletely established. Since the 1960s, when thermal analysis techniques were developed, studies of solid-state decompositions contributed to establishment of the new experimental techniques, but research interest became redirected towards increasing the capabilities of automated equipment to collect, to store and later to analyze rate changes for selected reactions. Subsequently, much less attention has been directed towards chemical features of the rate processes studied, which have included a range of reactants that is much more diverse than the simple solid-state reactions with which early thermokinetic studies were principally concerned. Moreover, the theory applied to these various reactants does not recognize the possible complexities of behaviour that may include mechanisms involving melting and/or concurrent/consecutive reactions, etc. The situation that has arisen following, and attributable to, the eclipse of solid-state decomposition studies by thermal analysis, is presented here and the consequences critically discussed in a historical context. It is concluded that methods currently used for kinetic and mechanistic investigations of all types of thermal reactions indiscriminately considered by the same, but inadequate theory, are unsatisfactory. Urgent and fundamental reappraisal of the theoretical foundations of thermokinetic chemical studies is now necessary and overdue. While there are important, but hitherto unrecognized, delusions in thermokinetic methods and theories, an alternative theoretical explanation that accounts for many physical and chemical features of crystolysis reactions has been proposed. However, this novel but general model for the thermal behaviour and properties of solids has similarly remained ignored by the thermoanalytical community. The objective of this article is to emphasize the now pressing necessity for an open debate between these unreconciled opinions of different groups of researchers. The ethos of science is that disagreement between rival theories can be resolved by experiment and/or discussion, which may also strengthen the foundations of the subject in the process. As pointed out below, during recent years there has been no movement towards attempting to resolve some fundamental differences of opinion in a field that lacks an adequate theory. This should be unacceptable to all concerned. Here some criticisms are made of specific features of the alternative reaction models available with the stated intention of provoking a debate that might lead to identification of the significant differences between the currently irreconciled views. This could, of course, attract the displeasure of both sides, who will probably criticise me severely. Because I intend to retire completely from this field soon, it does not matter to me if I am considered to be ‘wrong’, if it contributes to us all eventually agreeing to get the science ‘right’.     

Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER

In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.     

Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC‐MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes

Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel‐cutting, and quantitative LC‐MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an “overlap score,” (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 “overlap factors,” (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells.     

Application of the ETD/PTR reactions in top‐down proteomics as a faster alternative to bottom‐up nanoLC‐MS/MS protein identification

Our goal was to compare two popular analytical techniques used nowadays in proteomic investigations for proteins/peptides sequencing and identification, a widely used nanoLC‐MS/MS approach applied in the bottom‐up proteomics and electron transfer dissociation/proton transfer reaction fragmentation preferably used when top‐down strategy is applied. Comparison was carried out with the aid of the ESI‐quadrupole ion‐trap instrument using the following criteria: total time of analysis including sample preparation, sequence coverage, Mascot scoring, capability to detect modifications, quality of the results as a function of protein molecular weight and sample consumption. Copyright © 2012 John Wiley & Sons, Ltd.     

Native protein mapping and visualization of protein interactions in the area of human plasma high‐density lipoprotein by combining nondenaturing micro 2DE and quantitative LC‐MS/MS

A human plasma sample was subjected to nondenaturing micro 2DE and a gel area (5 mm × 18 mm) that includes high‐density lipoprotein (HDL) was cut into 1 mm × 1 mm squares, then the proteins in the 90 gel pieces were analyzed by quantitative LC‐MS/MS. Grid‐cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC‐MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data. Totally 154 proteins were assigned in the 90 gel pieces and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The map of apolipoprotein (Apo) A‐I showed a wide apparent mass distribution characteristic to HDL and was compared with the maps of the other 153 proteins. Eleven proteins showed maps of wide distribution that overlapped with the map of Apo A‐I, and all have been reported to be the components of HDL. Further, seven minor proteins associated with HDL were detected at the gel positions of high Apo A‐I quantity. These results for the first time visualized the localization of HDL apolipoproteins on a nondenaturing 2DE gel and strongly suggested their interactions.     

Development of a multiplex UPLC-MRM MS method for quantification of human membrane transport proteins OATP1B1, OATP1B3 and OATP2B1 in in vitro systems and tissues

OATP1B1, OATP1B3 and OATP2B1 are important members of the organic anion transporting polypeptides (OATP) family and are implicated in the hepatic disposition of endobiotics and xenobiotics. Quantitating the expression levels of human OATP1B1, OATP1B3 and OATP2B1 in in vitro systems and tissue samples could significantly improve attempts to scale up in vitro data and result in more effective in vitro–in vivo correlation of transporter-mediated effects on drug disposition, such as hepatic clearance. In the present study, a quantification method was developed, characterized, and implemented for simultaneous determination of human OATP1B1, OATP1B3 and OATP2B1 in HEK cells transfected with OATP-expressing plasmid vectors (SLCO1B1, SLCO1B3, and SLCO2B1, respectively), human hepatocytes, human brain capillary endothelial cells, and humanized mouse liver tissue using UPLC-MRM MS. Purified membrane protein standards prepared and characterized as previously reported (Protein Expr. Purif. 2008, 57, 163-71) were first used as standards for absolute quantification of the expression levels of the three human OATP membrane proteins. The specificity of the optimized MRM transitions were characterized by analyzing the tryptic digests of the membrane protein fraction of wild type HEK cells and control mouse liver tissue using the herein reported UPLC-MRM MS method. The linearity of the calibration curve spanned from 0.2 μg mL⁻¹ (0.040 μg mg⁻¹) to 20 μg mL⁻¹ (4.0 μg mg⁻¹), with accuracy (% RE) within 15% at all concentrations examined for all three OATPs of interest in this study. The intra- and inter-day assay accuracy (% RE) and coefficient of variations (% CV) of triplicates are all within 15% for all levels of quality control samples prepared by mixing the membrane fraction of control mouse liver tissue with the required amount of purified human OATP1B1, OATP1B3 and OATP2B1.     

A new HPLC–MS/MS method for the simultaneous quantification of SGLT2 inhibitors and metformin in plasma and its application to a pharmacokinetic study in healthy volunteers

Monitoring the plasma concentrations of metformin and sodium‐glucose cotransporter‐2 inhibitors (canagliflozin, dapagliflozin and empagliflozin) is essential for pharmacokinetic and bioequivalence studies and therapeutic monitoring. The present work therefore aimed to develop and validate a high‐performance liquid chromatography coupled to tandem mass spectrometry (HPLC–MS/MS) method for the simultaneous quantification of these drugs in human plasma. The analyses were performed using an Agilent 1200 HPLC system coupled to an Applied Biosystems API 3200 triple quadrupole MS/MS with electrospray ionization in positive ion mode. After one‐step protein precipitation of plasma with acetonitrile containing 0.1% formic acid, chromatographic separation was achieved on an Xbridge C₁₈ column, with a mobile phase consisting of a gradient of water and acetonitrile, both containing 1 mm ammonium formate and 0.1% formic acid. Quantification was performed in multiple reaction monitoring mode using m/z 130.1 → 71.1 for metformin, m/z 462.0 → 191.2 for canagliflozin, m/z 426.1 → 167.1 for dapagliflozin and m/z 468.0 → 354.9 for empagliflozin. The proposed method was validated and demonstrated to be adequate for the quantification of metformin, canagliflozin, dapagliflozin and empagliflozin for clinical monitoring, pharmacokinetics and bioequivalence studies.     

Optimisation of ICP-MS collision/reaction cell conditions for the determination of elements likely to be interfered (V, Cr, Fe, Co, Ni, As and Se) in foodstuffs

A strategy for the accurate determination in foodstuffs of seven elements liable to be interfered with (V, Cr, Fe, Co, Ni, As and Se), was successfully applied. Firstly, to reduce spectroscopic interferences, four influential factors (hexapole and quadrupole bias, helium and hydrogen flows) of the collision/reaction cell device were optimised through the experimental design methodology. Secondly, non-spectroscopic interferences, which may severely disturb the analysis of matrices containing large amounts of non-target elements, were significantly reduced by a limited decrease in the flow rate of the optimum initial nebuliser rather than with a specific time-consuming dilution. Finally, the optimised multi-element method was subjected to a full validation that demonstrated its acceptable analytical performance.     

Preparation of W1/O/W2 emulsion to limit the diffusion of Fe3+ in the Fricke gel 3D dosimeter

The irradiation of tumors in radiotherapy requires accurate 3D dosimetry. The Fricke 3D dosimeters, which were considered to be high potential of application in 3D dosimetry, suffer from a reduced temporal integrity of dose distribution caused by Fe³⁺ ions diffusion. To overcome the drawback, we firstly synthesized a kind of amphiphilic molecules with critical micelle concentration of 0.45 g/L and hydrophile‐lipophile balance value of 10, then prepared multiple emulsions by self‐assembling those molecules in Fricke solution under liquid paraffin, and finally obtained Fricke hydrogel embedded with the multiple emulsions. The diffusion coefficient of Fe³⁺ ions in the embedded Fricke hydrogel was measured to be 0.17 mm²/h. The hydrogel dosimeter exhibits considerable potential for use in dose verification applications.