高效液相色谱-串联质谱检测基因组DNA甲基化方法的建立

目的:建立高效液相色谱-串联质谱(HPLC-ESI-MS/MS)检测基因组DNA甲基化水平的方法。方法:以5-mdC和dG为标准品,采用全自动高效液相色谱系统进行分离,串联电喷雾质谱检测,选择多反应监测模式(MRM)测定标准品,绘制标准工作曲线。结果:在MRM模式下选取5-mdC(m/z 241.9→126.3)和dG(m/z 268.1→152.3)分别作为定量检测的母子离子对,各化合物能实现良好的基线分离;5-mdC和dG碰撞能均为15 eV,去簇电压分别为40和45 V,最低定量限分别为1.65和2.47 fmol;标准品的响应值比为90%~110%;5-mdC含量的天内相对标准偏差和天间相对标准偏差均小于8%。结论:HPLC-ESI-MS/MS是能应用于检测基因组DNA甲基化的一种高通量、高准确率、高分辨率、高灵敏度且重复性好的方法。     

基于液相色谱质谱联用的蛋白质组非标记定量研究策略的建立及应用

定量蛋白质组研究是蛋白质组研究的热点和难点,而液相色谱质谱技术已经被广泛地应用于蛋白质的定性和定量研究.该研究建立和优化了一种基于液相色谱质谱联用技术的蛋白质组非标记定量方法,并对两种肽段质谱检测计数的归一化算法进行了比较,结果发现ASC法要优于Rsc法.最后,将建立的方法应用于肝癌细胞模型HepG2和HepG2-HBx细胞系的差异蛋白质组表达研究.质谱鉴定结果用聚类分析软件cluster3.0进行分析,最后鉴定出107个重叠蛋白,其中9个蛋白质表达上调(Ratio>1.75),6个蛋白质表达下调(Ratio<0.5),这些蛋白质均与肝癌发生和恶化密切相关.结果表明,该技术操作简单、方便,具有较高的灵敏度和动态范围,利用该方法进行差异蛋白质组研究和发现生物标志物在理论和临床上具有十分重要的意义.     

硝酸纤维膜和丙酮沉淀尿蛋白质保存方法的比较

硝酸纤维膜法是一种简单、快速、经济的尿液蛋白质保存方法,但其与传统尿液蛋白质丙酮沉淀方法的差异有待进一步研究。相同尿液分别经硝酸纤维膜法和丙酮沉淀法制备尿蛋白质,经液相串联质谱分析鉴定蛋白质,采用谱图数定量,研究两种不同方法的差别。结果显示硝酸纤维膜法和丙酮沉淀法鉴定蛋白质数目几乎相同,鉴定蛋白质在谱图数的分布上几乎相同,鉴定蛋白质在蛋白质变异系数的分布上也几乎相同。因此,硝酸纤维膜法处理尿蛋白质与丙酮沉淀法基本一致,可以应用于大规模临床尿液样本的保存。     

iTRAQ多重化学标记串联质谱技术在比较蛋白质组学中的应用

研究不同生理和病理条件下细胞内蛋白质的含量和状态变化是比较蛋白质组学的核心内容。要揭示上述动态过程往往需要进行多个样品的同步比较分析。近年来,在体内和体外同位素标记基础上,用多维液相色谱分离多肽,进而用串联质谱进行相对定量的分析方法已成为高通量比较蛋白质组研究的主要手段之一。该文就目前唯一一种可以进行四重蛋白质样品同步比较的iTRAQ标记-串联质谱分析技术进行综述。     

iTRAQ结合2D LC-MS/MS技术在草菇不同生长发育时期蛋白质组分析中的应用

【目的】旨在采用iTRAQ标记结合二维液相色谱串联质谱技术对草菇不同生长发育阶段的差异蛋白质组进行研究。【方法】首先将提取的草菇不同生长阶段蛋白样品进行SDS-PAGE分析,其次将经二维液相色谱串联质谱技术获取的串联质谱数据通过MASCOT软件搜库,之后对鉴定蛋白质数据进行了主成分分析(Principal componentanalysis,PCA)、层次聚类(Hierarchy clustering)分析、K-均值(K-means)聚类和GeneOntology(GO)注释分析。【结果】试验结果显示,共计获得2 335个不同肽段,鉴定到1 039个蛋白质,其中1 030个蛋白质具有定量信息。在子实体阶段中显著上调蛋白质64个,下调蛋白质150个。生物信息学分析表明,iTRAQ标记技术结合二维液相色谱串联质谱可对不同生长发育时期的草菇蛋白样品进行有效地分离和鉴定。【结论】这一研究结果为深入研究草菇乃至其他大型担子菌子实体形成和发育的分子机制提供借鉴。     

6硝酸纤维膜和丙酮沉淀尿蛋白质保存方法的比较

硝酸纤维膜法是一种简单、快速、经济的尿液蛋白质保存方法,但其与传统尿液蛋白质丙酮沉淀方法的差异有待进一步研究。相同尿液分别经硝酸纤维膜法和丙酮沉淀法制备尿蛋白质,经液相串联质谱分析鉴定蛋白质,采用谱图数定量,研究两种不同方法的差别。结果显示硝酸纤维膜法和丙酮沉淀法鉴定蛋白质数目几乎相同,鉴定蛋白质在谱图数的分布上几乎相同,鉴定蛋白质在蛋白质变异系数的分布上也几乎相同。因此,硝酸纤维膜法处理尿蛋白质与丙酮沉淀法基本一致,可以应用于大规模临床尿液样本的保存。     

草菇子实体不同成熟阶段的比较蛋白质组学分析

采用iTRAQ标记结合二维液相色谱串联质谱技术对草菇不同成熟阶段的差异蛋白质组进行研究。首先将提取的草菇不同成熟阶段蛋白样品进行SDS-PAGE分析,其次将经二维液相色谱串联质谱技术获取的串联质谱数据通过MASCOT软件搜库,之后对鉴定蛋白质数据进行了KEGG代谢通路分析。试验共计获得2 335个不同肽段, 鉴定到1 039个蛋白质,其中1 030个蛋白质具有定量信息。与蛋形期相比,在伸长期和成熟期阶段显著上调蛋白质85个,下调蛋白质103个。KEGG代谢通路分析结果显示,草菇不同成熟阶段中的68个差异蛋白质可定位于4种伞菌目模式真菌（灰盖鬼伞、双色蜡蘑、可可丛枝病菌和裂褶菌）的45个不同生物代谢途径,全景展示出草菇成熟阶段差异表达蛋白质定位的代谢网络。结果表明,iTRAQ标记技术结合二维液相色谱串联质谱可对不同生长发育时期的草菇蛋白样品进行有效地分离和鉴定。     

分散固相萃取剂-液相色谱串联质谱法测定鸡肉和鸡蛋中氟苯尼考和氟苯尼考胺残留

建立分散固相萃取剂-液相色谱串联质谱法(HPLC-MS/MS)同时检测鸡肉及鸡蛋中氟苯尼考和氟苯尼考胺的方法.样品用乙腈提取,C18分散固相萃取填料净化,乙腈饱和的正己烷脱脂,电喷雾离子源正负模式切换,HPLC-MS/MS多反应监测(MRM),同位素内标法定量.氟苯尼考和氟苯尼考胺线性范围分别为0.1 ng/mL～2....     

一种用高效液相色谱-电喷雾/串联质谱(HPLC-ESI/MSn)定量检测植物组织中微量1-氨基环丙烷-1-羧酸(ACC)含量的方法

介绍一种用高效液相色谱碳18柱(HPLC-C18)分离.电喷雾串联质谱(ESI-MSn)鉴定和定量检测植物组织中微量1-氨基环丙烷-1-羧酸(ACC)含量的方法,其最低检测限达0.7 pmol,标准曲线线性符合系数为0.9992.建立了从20～100 mg微量植物样品中提取ACC和固相萃取(SPE)预纯化的方法,加样回收率为95.1%±4.2%.此种提取方法结合HPLC-ESI/MSn分析与定性定量检测苹果'2001富士'中ACC含量为306.6 ng·g-1(FW),表明此法适合于定性定量检测植物样品中的微量ACC.     

LC-MS/MS法同时测定大鼠血浆中地榆皂苷Ⅰ和地榆皂苷Ⅱ的血药浓度及其药代动力学

采用液相色谱-串联质谱法(LC-MS/MS)同时测定大鼠血浆中的地榆皂苷Ⅰ和地榆皂苷Ⅱ,并在此基础上研究这两种活性物质在大鼠体内的药代动力学。样品前处理采用沉淀蛋白法,选用Ultimate XB-C8色谱柱(100 mm×2.1 mm,3μm,Welch,USA),采用Sciex 4000 Q-TRAP型三重四级杆串联质谱,电喷雾(ESI)源,多级反应监测(MRM)负离子模式。血浆中地榆皂苷Ⅰ和地榆皂苷Ⅱ的标准曲线线性范围均为1～2 000 ng/mL(相关系数R0.995),本方法灵敏、快速且稳定。大鼠口服给予地榆标准品后,吸收较快,绝对生物利用度(F_(abs))较小。所建立的方法可准确、快速、灵敏地检测大鼠血浆中地榆皂苷Ⅰ和地榆皂苷Ⅱ的血药浓度,适用于临床前的药代动力学研究。     

High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites

The detection and quantification of plasma (serum) proteins at or below the ng/ml concentration range are of critical importance for the discovery and evaluation of new protein biomarkers. This has been achieved either by the development of high sensitivity ELISA or other immunoassays for specific proteins or by the extensive fractionation of the plasma proteome followed by the mass spectrometric analysis of the resulting fractions. The first approach is limited by the high cost and time investment for assay development and the requirement of a validated target. The second, although reasonably comprehensive and unbiased, is limited by sample throughput. Here we describe a method for the detection of plasma proteins at concentrations in the ng/ml or sub-ng/ml range and their accurate quantification over 5 orders of magnitude. The method is based on the selective isolation of N-glycosites from the plasma proteome and the detection and quantification of targeted peptides in a quadrupole linear ion trap instrument operated in the multiple reaction monitoring (MRM) mode. The unprecedented sensitivity of the mass spectrometric analysis of minimally fractionated plasma samples is the result of the significantly reduced sample complexity of the isolated N-glycosites compared with whole plasma proteome digests and the selectivity of the MRM process. Precise quantification was achieved via stable isotope dilution by adding (13)C- and/or (15)N-labeled reference analytes. We also demonstrate the possibility of significantly expanding the number of MRM measurements during one single LC-MS run without compromising sensitivity by including elution time constraints for the targeted transitions, thus allowing quantification of large sets of peptides in a single analysis.     

The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments

Background  

Isotope-coded affinity tags (ICAT) is a method for quantitative proteomics based on differential isotopic labeling, sample digestion and mass spectrometry (MS). The method allows the identification and relative quantification of proteins present in two samples and consists of the following phases. First, cysteine residues are either labeled using the ICAT Light or ICAT Heavy reagent (having identical chemical properties but different masses). Then, after whole sample digestion, the labeled peptides are captured selectively using the biotin tag contained in both ICAT reagents. Finally, the simplified peptide mixture is analyzed by nanoscale liquid chromatography-tandem mass spectrometry (LC-MS/MS). Nevertheless, the ICAT LC-MS/MS method still suffers from insufficient sample-to-sample reproducibility on peptide identification. In particular, the number and the type of peptides identified in different experiments can vary considerably and, thus, the statistical (comparative) analysis of sample sets is very challenging. Low information overlap at the peptide and, consequently, at the protein level, is very detrimental in situations where the number of samples to be analyzed is high.     

Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification

Verification of candidate biomarker proteins in blood is typically done using multiple reaction monitoring (MRM) of peptides by LC-MS/MS on triple quadrupole MS systems. MRM assay development for each protein requires significant time and cost, much of which is likely to be of little value if the candidate biomarker is below the detection limit in blood or a false positive in the original discovery data. Here we present a new technology, accurate inclusion mass screening (AIMS), designed to provide a bridge from unbiased discovery to MS-based targeted assay development. Masses on the software inclusion list are monitored in each scan on the Orbitrap MS system, and MS/MS spectra for sequence confirmation are acquired only when a peptide from the list is detected with both the correct accurate mass and charge state. The AIMS experiment confirms that a given peptide (and thus the protein from which it is derived) is present in the plasma. Throughput of the method is sufficient to qualify up to a hundred proteins/week. The sensitivity of AIMS is similar to MRM on a triple quadrupole MS system using optimized sample preparation methods (low tens of ng/ml in plasma), and MS/MS data from the AIMS experiments on the Orbitrap can be directly used to configure MRM assays. The method was shown to be at least 4-fold more efficient at detecting peptides of interest than undirected LC-MS/MS experiments using the same instrumentation, and relative quantitation information can be obtained by AIMS in case versus control experiments. Detection by AIMS ensures that a quantitative MRM-based assay can be configured for that protein. The method has the potential to qualify large number of biomarker candidates based on their detection in plasma prior to committing to the time- and resource-intensive steps of establishing a quantitative assay.     

An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology

Selected reaction monitoring (SRM) is an accurate quantitative technique, typically used for small-molecule mass spectrometry (MS). SRM has emerged as an important technique for targeted and hypothesis-driven proteomic research, and is becoming the reference method for protein quantification in complex biological samples. SRM offers high selectivity, a lower limit of detection and improved reproducibility, compared to conventional shot-gun-based tandem MS (LC-MS/MS) methods. Unlike LC-MS/MS, which requires computationally intensive informatic postanalysis, SRM requires preacquisition bioinformatic analysis to determine proteotypic peptides and optimal transitions to uniquely identify and to accurately quantitate proteins of interest. Extensive arrays of bioinformatics software tools, both web-based and stand-alone, have been published to assist researchers to determine optimal peptides and transition sets. The transitions are oftentimes selected based on preferred precursor charge state, peptide molecular weight, hydrophobicity, fragmentation pattern at a given collision energy (CE), and instrumentation chosen. Validation of the selected transitions for each peptide is critical since peptide performance varies depending on the mass spectrometer used. In this review, we provide an overview of open source and commercial bioinformatic tools for analyzing LC-MS data acquired by SRM.     

Development and validation of a quantitative assay for the measurement of two HIV-fusion inhibitors, enfuvirtide and tifuvirtide, and one metabolite of enfuvirtide (M-20) in human plasma by liquid chromatography-tandem mass spectrometry

A method for the quantification of two peptide HIV-1 fusion inhibitors (enfuvirtide, T-20 and tifuvirtide, T-1249) and one metabolite of enfuvirtide (M-20) in human plasma has been developed and validated, using liquid chromatography coupled with electrospray tandem mass spectrometry (LC-MS/MS). The analytes were extracted from plasma by solid-phase extraction (SPE) on vinyl-copolymer cartridges. Chromatographic separation of the peptides was performed on a Symmetry 300 C(18) column (50mmx2.1mm I.D., particle size 3.5 microm), using a water-acetonitrile gradient containing 0.25% (v/v) formic acid. The triple quadrupole mass spectrometer was operated in the positive ion-mode and multiple reaction monitoring (MRM) was used for peak detection. Deuterated (d60) enfuvirtide and (d50) tifuvirtide were used as internal standards. The assay was linear over a concentration range of 20-10,000 ng/ml for enfuvirtide and tifuvirtide and of 20-2000 ng/ml for M-20. Intra- and inter-assay precisions and deviations from the nominal concentrations were 相似文献   

Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach

The availability of label-free data derived from yeast cells (based on the summed intensity of the three strongest, isoform-specific peptides) permitted a preliminary assessment of protein abundances for glycolytic proteins. Following this analysis, we demonstrate successful application of the QconCAT technology, which uses recombinant DNA techniques to generate artificial concatamers of large numbers of internal standard peptides, to the quantification of enzymes of the glycolysis pathway in the yeast Saccharomyces cerevisiae. A QconCAT of 88 kDa (59 tryptic peptides) corresponding to 27 isoenzymes was designed and built to encode two or three analyte peptides per protein, and after stable isotope labeling of the standard in vivo, protein levels were determined by LC-MS, using ultra high performance liquid chromatography-coupled mass spectrometry. We were able to determine absolute protein concentrations between 14,000 and 10 million molecules/cell. Issues such as efficiency of extraction and completeness of proteolysis are addressed, as well as generic factors such as optimal quantotypic peptide selection and expression. In addition, the same proteins were quantified by intensity-based label-free analysis, and both sets of data were compared with other quantification methods.     

Analysis of host-cell proteins in biotherapeutic proteins by comprehensive online two-dimensional liquid chromatography/mass spectrometry

Assays for identification and quantification of host-cell proteins (HCPs) in biotherapeutic proteins over 5 orders of magnitude in concentration are presented. The HCP assays consist of two types: HCP identification using comprehensive online two-dimensional liquid chromatography coupled with high resolution mass spectrometry (2D-LC/MS), followed by high-throughput HCP quantification by liquid chromatography, multiple reaction monitoring (LC-MRM). The former is described as a “discovery” assay, the latter as a “monitoring” assay. Purified biotherapeutic proteins (e.g., monoclonal antibodies) were digested with trypsin after reduction and alkylation, and the digests were fractionated using reversed-phase (RP) chromatography at high pH (pH 10) by a step gradient in the first dimension, followed by a high-resolution separation at low pH (pH 2.5) in the second dimension. As peptides eluted from the second dimension, a quadrupole time-of-flight mass spectrometer was used to detect the peptides and their fragments simultaneously by alternating the collision cell energy between a low and an elevated energy (MSE methodology). The MSE data was used to identify and quantify the proteins in the mixture using a proven label-free quantification technique (“Hi3” method). The same data set was mined to subsequently develop target peptides and transitions for monitoring the concentration of selected HCPs on a triple quadrupole mass spectrometer in a high-throughput manner (20 min LC-MRM analysis). This analytical methodology was applied to the identification and quantification of low-abundance HCPs in six samples of PTG1, a recombinant chimeric anti-phosphotyrosine monoclonal antibody (mAb). Thirty three HCPs were identified in total from the PTG1 samples among which 21 HCP isoforms were selected for MRM monitoring. The absolute quantification of three selected HCPs was undertaken on two different LC-MRM platforms after spiking isotopically labeled peptides in the samples. Finally, the MRM quantitation results were compared with TOF-based quantification based on the Hi3 peptides, and the TOF and MRM data sets correlated reasonably well. The results show that the assays provide detailed valuable information to understand the relative contributions of purification schemes to the nature and concentrations of HCP impurities in biopharmaceutical samples, and the assays can be used as generic methods for HCP analysis in the biopharmaceutical industry.     

Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards

A general method for the quantification of proteins in human serum was developed using mass spectrometry (MS) and stable isotope-labeled synthetic peptides as internal standards. Using this approach, C-reactive protein (CRP), a diagnostic marker of rheumatoid arthritis (RA), was detected in serum samples taken from patients with either erosive or nonerosive RA and compared to healthy individuals. Small volumes of serum samples were enriched for low-abundance proteins through the selective removal of human serum albumin (HSA), immunoglobulin G (IgG), and haptoglobin. After depletion of abundant proteins, the complexity of the protein mixture was further simplified using size exclusion chromatography (SEC) to fractionate denatured proteins into discrete molecular weight ranges. Fractions of interest containing CRP, M(r) = 25 000, were pooled, digested with trypsin, and then fixed quantities of the synthetic peptides were added to the mixture. The mixture of tryptic peptides was subsequently analyzed by nanoflow chromatography-tandem MS (nanoLC-MS/MS) using multiple-reaction monitoring (MRM) on a triple quadrupole mass spectrometer (TQ-MS). The ratio of transition ions derived from the endogenous and isotope-labeled peptides provided a quantitative measure of CRP in the original samples as assessed by independent measurement of CRP in the same patient samples using an immunoassay. The use of isotope-labeled synthetic peptides and MRM is a powerful analytical method for the prescreening of candidate protein biomarkers in human serum prior to antibody and immunoassay development.     

P23-M Limit of Quantitation for Low-Abundance Proteins in Plasma by Targeted MS

Biomarker discovery results in the creation of candidate lists of potential markers that must be subsequently verified in plasma.¹ The most mature methods at present require abundant protein depletion and fractionation at the protein/peptide levels in order to detect and quantitate low ng/mL concentrations of plasma proteins by stable isotope dilution mass spectrometry. Sample-processing methods with sufficient throughput, recovery, and reproducibility to enable robust detection and quantitation of candidate bio-marker proteins were evaluated by adding five non-native proteins to immunoaffinity-depleted female plasma at varying concentrations (1000, 100, 50, 25, and 10 ng/mL). Each protein was monitored by one or more representative synthetic tryptic peptides labeled with [¹³C₆]leucine or [¹³C₅] valine. Following reduction, carbamidomethylation, and enzymatic digestion, two separate processing paths were compared. In path 1, digested plasma was diluted 1:10 and [¹³C] internal standards were added just prior to direct analysis by multiple reaction monitoring with LC-MS/MS (MRM LC-MS/MS). In path 2, peptides were separated by strong cation exchange, and [¹³C] internal standards were added to corresponding SCX fractions prior to analysis by MRM LC-MS/MS. Detection and quantitation by MRM used the response of at least two product ions from each of the signature peptides. Using processing path 1, we achieved detection and quantitation down to 50 ng/mL in depleted plasma. However, using processing path 2, we achieved detection and quantitation of all spiked proteins, including the non-native protein at 10 ng/mL. While analysis of non-fractionated plasma achieved higher recovery of those proteins detected in both processes, SCX fractionation at the peptide level clearly increases detection and LOQs for potential biomarker proteins in plasma.     

A rugged and accurate liquid chromatography-tandem mass spectrometry method for quantitative determination of BMS-790052 in plasma

To support toxicokinetic assessments, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the quantification of BMS-790052 in rat, dog, monkey, rabbit and mouse K(2)EDTA plasma. The drug was isolated from buffered samples using ISOLUTE C8 96-well solid phase extraction (SPE) plates. Chromatographic separation was achieved on a Waters Atlantis dC18 analytical column (2.1 mm × 50 mm, 5 μm) with detection accomplished using an API 4000 tandem mass spectrometer in positive ion electrospray and multiple reaction monitoring (MRM) mode. The standard curves, which ranged from 5.00 to 2000 ng/mL for BMS-790052, were fitted to a 1/x(2) weighted linear regression model. The intra-assay precision (%CV) and inter-assay precision (%CV) were within 8.5%, and the assay accuracy (%Dev) was within ±7.1 for rat, dog, monkey, rabbit and mouse K(2)EDTA plasma. This accurate, precise, and selective SPE/LC-MS/MS method has been successfully applied to analyze several thousands of non-clinical study samples.