Evaluation of isotope-coded protein labeling (ICPL) in the quantitative analysis of complex proteomes

An evaluation of the ICPL (isotope-coded protein labeling) non-isobaric labeling technique was performed using two different biological models. Two samples containing phage T4 capsids were mixed in a 1:1 ratio after being labeled with the light or heavy versions of the ICPL reagent. The analysis of this proteome demonstrated the feasibility of this approach for differential quantitative proteomics and was employed to optimize the experimental parameters of the ICPL workflow. ICPL-mediated analysis of two more complex proteomes, those of a Salmonella enterica serovar Typhimurium virulent strain and an isogenic attenuated mutant, and its comparison with the results obtained in a 2D-PAGE “classical” approach confirmed that ICPL is a valuable alternative to other labeling techniques currently in use. In addition, our results suggest that labeling at the peptide level instead of following the standard ICPL workflow should increase both the number of proteins quantified and the reliability of the quantification.     

基于稳定同位素标记与质谱分析的蛋白质定量算法研究进展

蛋白质定量研究已成为蛋白质组学的热点,它是疾病相关生物标志物发现的重要途径.基于稳定同位素标记的质谱分析技术是蛋白质定量最常用的方法之一.随着实验方法的发展和改进,定量数据处理方法也在不断更新与完善.一般来说,定量数据处理包括四步:搜库鉴定、图谱定量信息提取与计算、肽段丰度比计算和蛋白质丰度比计算及差异显著性分析,其中后三步是数据处理的核心.目前,后三步中每步都有多种可选算法,这些算法一般都是针对特定实验技术而提出的,缺乏深入的工作对它们进行系统比较和优化.为此,在总结目前主要实验技术方法的基础上,论述了定量算法的现状和存在问题,并针对一些问题提出了可行的解决办法.     

Vibrational isotope effect by the low rank perturbation method

Mathematical formalism of the Low Rank Perturbation method (LRP) is applied to the vibrational isotope effect in the harmonic approximation with a standard assumption that force field does not change under isotopic substitutions. A pair of two n-atom isotopic molecules A and B which are identical except for isotopic substitutions at ρ atomic sites is considered. In the LRP approach vibrational frequencies ω _k and normal modes of the isotopomer B are expressed in terms of the vibrational frequencies ν _i and normal modes of the parent molecule A. In those relations complete specification of the normal modes is not required. Only amplitudes at sites τ affected by the isotopic substitutions and in the coordinate direction s (s = x, y, z) are needed. Out-of-plane vibrations of the (H,D)-benzene isotopomers are considered. Standard error of the LRP frequencies with respect to the DFT frequencies is on average . This error is due to the uncertainty of the input data (± 0.5 cm⁻¹) and in the absence of those uncertainties and in the harmonic approximation it should disappear. In comparing with experiment, one finds that LRP frequencies reproduces experimental frequencies of (H,D)-benzene isotopomers better () than scaled DFT frequencies () which are designed to minimize (by frequency scaling technique) this error. In addition, LRP is conceptually and numerically simple and it also provides a new insight in the vibrational isotope effect in the harmonic approximation.     

Bicyclic imidazolium-based ionic liquids: synthesis and characterization

We previously reported the use of imidazole as starting compound for preparing a bicyclic imidazolium ionic liquid, [b-3C-im][NTf₂], with an overall 29% isolated yield in four synthetic steps. This new room temperature ionic liquid was shown to be far more chemically stable than commonly used [bmim][PF₆], [bdmim][PF₆], and [bdmim][NTf₂]. Because of this intriguing chemical stability, it prompted us to develop a more generalized and high yielding synthesis so that molecular diversity of bicyclic ionic liquids may be explored. In this work, we amended the previous synthetic route by employing 4-chlorobutyronitrile or 5-chlorovaleronitrile as starting materials and successfully developed a five-step synthesis of a series of novel bicyclic imidazolium-based ionic liquids in 40-53% overall isolated yields. We investigated intrinsic reactivity of all bicyclic ionic liquids prepared and found that, under strongly basic conditions, among all tested ionic liquids the 5,5-membered [R-3C-im][NTf₂] ionic liquids were most stable to solvent deuterium isotope exchange while the previously reported [bdmim][NTf₂] ionic liquid was 50% deuterium exchanged at its C-2 methyl in 30 min at ambient temperature. Under identical condition, the commonly used [bmim][NTf₂] ionic liquid was deuterium exchanged instantaneously at its C-2 hydrogen. In the absence of bases, only [bmim][PF₆] was deuterium exchanged (50% within 1 h) and all other ionic liquids gave no detectable exchanges even after 25 days at ambient temperature. Moreover, both [bmim][NTf₂] and [bdmim][NTf₂] ionic liquids were readily methylated at C-2 position with methyl iodide under basic condition at room temperature. Under the same condition, [R-3C-im][NTf₂] and [R-4C-im][NTf₂] ionic liquids were completely stable and chemically inert. We envisioned that [R-3C-im][NTf₂] should be well suited as solvents for organic synthesis.     

Urinary exposure marker discovery for toxicants using ultra-high pressure liquid chromatography coupled with Orbitrap high resolution mass spectrometry and three untargeted metabolomics approaches

Human biomonitoring is the assessment of actual internal contamination of chemicals by measuring exposure markers, chemicals or their metabolites, in human urine, blood, serum, and other body fluids. However, the metabolism of chemicals within an organism is extremely complex. Therefore, the identification of metabolites is often difficult and laborious. Several untargeted metabolomics methods have been developed to perform objective searching/filtering of accurate-mass-based LC-MS data to facilitate metabolite identification. In this study, three metabolomics data processing approaches were used for chemical exposure marker discovery in urine with an LTQ-Orbitrap high-resolution mass spectrometry (HRMS) dataset; di-isononyl phthalate (DINP) was used as an example. The data processing techniques included the SMAIT, mass defect filtering (MDF), and XCMS Online. Sixteen, 83, and 139 probable DINP metabolite signals were obtained using the SMAIT, MDF, and XCMS procedures, respectively. Fourteen probable metabolite signals mined simultaneously by the three metabolomics approaches were confirmed as DINP metabolites by structural information provided by LC-MS/MS. Among them, 13 probable metabolite signals were validated as exposure-related markers in a rat model. Six (m/z 319.155, 361.127, 373.126, 389.157, 437.112 and 443.130) of the 13 exposure-related DINP metabolite signals have not previously been reported in the literature. Our data indicate that SMAIT provided an efficient method to discover effectively and systematically urinary exposure markers of toxicant. The DINP metabolism information can provide valuable information for further investigations of DINP toxicity, toxicokinetics, exposure assessment, and human health effects.     

~(12)CO_2/~(13)CO_2体系中碳同位素的显微激光拉曼光谱研究

采用自行设计的装置制备了一系列不同比例的12CO2/13 CO2混合物,对混合物样品进行显微激光拉曼测试,获得CO2气体碳同位素分子的拉曼特征峰。对实验数据分析发现,12CO2的摩尔分数[x(12CO2)]与12CO2/13 CO2混合物中拉曼特征峰峰面积比之间存在数学关系式。根据拟合的关系式,利用显微激光拉曼光谱可以预测CO2气体碳同位素的组成,并为以后预测单个流体包裹体中12CO2的摩尔分数奠定了理论基础。     

Effect of H/D isotope substitution on polarizability of methanol molecules

The electron polarizabilities (α₀·10²⁴/cm³ molec.⁻¹) were estimated from the data on refractive indices and molar volumes of H/D isotopomers of methanol at 25 °C using the Lorentz-Lorentz formula: 3.265 (CH₃OH), 3.260 (CH₃OD), 3.235 (CD₃OH), and 3.231 (CD₃OD). A relationship between the isotope effects for α₀ and volume (packing) changes in the structure of liquid methanol induced by deuterosubstitution in the methanol molecule was proposed. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1927–1928, August, 2005.     

Classifying wine according to geographical origin via quadrupole-based ICP–mass spectrometry measurements of boron isotope ratios

The potential of quadrupole-based ICP–MS as a tool for B-isotopic analysis of wines and its usefulness in provenance determinations were assessed. A precision of 0.1–0.25% RSD (corresponding to a relative standard deviation of the mean of three replicate measurements of 0.06–0.12%) was sufficient to establish small differences in the B isotope ratios in wines from different geographical origins. Each sample measurement was bracketed by measurements of a standard and mass bias drift correction made by interpolation. Sample preparation was kept to a minimum to avoid possible fractionation. Dilution of the wine samples by a factor of 100 with 0.65% HNO₃ was found to reduce matrix-induced mass discrimination substantially. Wines from three wine-producing regions, Stellenbosch, Robertson, and Swartland, in the Western Cape Province of South Africa, and wines from specific regions in France (Bergerac) and Italy (Valpolicella) were analyzed by ICP–QMS for their B-isotopic compositions. It was concluded that the ¹¹B/¹⁰B ratios can be used to characterize wines from different geographical origins. Average ¹¹B/¹⁰B ratios in red wines from South Africa (Stellenbosch), France (Bergerac), and Italy (Valpolicella) were found to differ by between 0.5 and 1.5%.     

飞秒激光剥蚀-多接收等离子体质谱原位分析玄武岩玻璃样品Mg同位素组成

建立了飞秒激光剥蚀多接收等离子体质谱(fsLA-MC-ICP-MS)原位微区分析玄武岩玻璃中Mg同位素的方法.溶液进样-干气溶胶条件下浓度匹配实验表明,样品和标准样品中Mg浓度比在0.4 ～3.0时,可获得准确样品Mg同位素组成.激光剥蚀条件对Mg同位素的准确测定有明显的影响,激光剥蚀斑束和扫描速率变化,使得质谱仪的质量歧视效应随进样负载量不同而产生较大的变化,并影响样品Mg同位素组成;激光剥蚀频率与δ25 Mg正相关,与δ26 Mg负相关,当剥蚀频率大于4 Hz时,δ25 Mg和δ26 Mg趋于平稳;超快激光的能量密度对Mg同位素组成影响较小.利用本方法对国际标准样品的分析结果与参考值在误差范围内一致.本方法具有制样简单、快速的特点,且测试结果准确可靠,为火山玻璃中Mg同位素分析提供了有效的分析手段.     

Enhanced Kinetic Isotope Effect of the Phosphate-Catalyzed Proton Exchange in N,N'-Dimethylurea

The concerted mechanism of phosphate-catalyzed proton exchange in N,N'-dimethylurea has been studied. Kinetic data were measured using the technigue of NMR line-shape analysis. A significant kinetic isotope effect was observed for the concerted proton transfer in N,N'-dimethylurea and is attributed to the tunnelling effect.