用EM算法改进鸟枪法蛋白质鉴定中的无标记定量方法

蛋白质定量是探索疾病发生发展状况和寻找新药靶标的重要手段。在shotgun蛋白组学中,目前常用定量方法包括综合同位素标记后的质谱峰强度方法和无标记定量方法。根据数据类型无标记定量方法可以分为两类:基于鉴定蛋白的质谱数的方法和基于质谱峰强度的方法。本研究主要用EM算法改进基于鉴定蛋白质谱数的定量方法,并用免疫印迹实验获得的酵母全蛋白的丰度来验证EM算法改进后定量的有效性结果表明,改进后的质谱数和蛋白丰度的相关性比改进前有一定的提高。同时,利用这些数据对主要的几种基于鉴定蛋白的质谱数的模型进行了比较,发现PAI模型最好,SpS模型次之,emPAI模型最不适合于蛋白质定量。     

基于稳定同位素标记的蛋白质组学定量方法研究进展

定量蛋白质组学已经成为后基因时代的重要研究方向之一。目前该领域的研究主要采用无标记定量方法和稳定同位素标记定量法。其中,基于稳定同位素标记的蛋白质组定量方法发展非常迅速,已为生命科学研究提供了重要的技术支撑。本文分析了基于稳定同位素标记的蛋白质组学定量方法,包括相对定量方法和绝对定量方法,并对其发展进行了展望。     

定量蛋白质组学分析方法

精确测量多个不同生理或病理条件下生物样本中蛋白质表达量的变化是定量蛋白质组学(quantitative proteomics)研究的重要内容。与传统的蛋白质定量方法(见表1)相比,组学规模的蛋白质定量可以实现在一次实验中对成百上千个蛋白质的定量测定和比较分析,为规模化发现和验证疾病诊断的生物标志物以及发展新的药物靶标提供了重要手段。     

高效毛细管电泳-电荷耦合器件检测器联用技术研究(Ⅲ)──定量计算方法

提出了加和峰高和峰体积法,并用于多波长电泳图的定量计算。将得到定性信息后的三维电泳图经峰加和等数据处理,转变成二维电泳图进行定量计算,提高了测定灵敏度、信噪比和计算结果的准确度与精密度。     

高效毛细管电泳—电荷耦合器件检测器联用技术研究

提出了加和峰高和峰体积法，并用于多波长电泳图的定量计算，将得到定性信息后的三维电泳图经和等数据处理，转变成二维电泳图进行定量计算，提高了测定灵敏度、信噪比和计算结果的准确度和精密度。     

电子亲合力与诱导效应的定量关系

本文提出了电子亲合力与诱导效应之间的定量关系。通过计算说明了电子亲合力与诱导效应的定量相关比电负性与诱导效应的定量相关好得多；并应用其定量关系式预测尚未实测到的取代基的电子亲合力值；根据计算结果, 可从不同实验方法测得的电子亲合力值中选择正确的实验值。该定量关系式能更加准确和定量地表征出诱导效应的作用。     

近红外成像用于双向电泳前的蛋白质快速定量

双向电泳(Two-dimensional Electrophoresis,2D)是蛋白质组学研究过程中的常用技术,而蛋白质样品的准确定量是做好双向电泳的前提条件。由于双向电泳的蛋白质样品在定量时存在试剂兼容性的问题,故需使用GE或Bio-rad公司研发的双向电泳专用蛋白质定量试剂盒,但此类试剂盒价格高昂且操作繁琐,因此亟待开发一种快速、准确、成本低廉的蛋白质定量方法。通过研究发现,蛋白质溶液与考马斯亮蓝-G250混合后,在近红外荧光成像系统680nm波长下可以被激发出荧光,且当蛋白质浓度在0.01~0.2mg·mL~(-1)范围内时,其荧光强度与蛋白质浓度具有很好的线性关系。基于此特点,建立了一种以96孔板为载体,利用近红外成像技术对蛋白质样品进行定量的方法,该方法可用于双向电泳前蛋白质样品的快速定量。     

基于质谱技术蛋白质定量方法的研究进展

质谱技术已经成为目前蛋白质鉴定的重要工具。定量分析细胞内蛋白质组的动态变化,是当前研究蛋白质功能、揭示细胞生物机理、寻找疾病蛋白标记物和药物靶标的迫切需要。本文综述了基于质谱技术蛋白质定量的策略、方法和应用等方面近年来的进展,评述了几种蛋白质质谱定量方法的特点和应用潜力。     

热分析-质谱联用中逸出气体的脉冲热分析定量方法

利用脉冲热分析技术(PulseTA)实现对热分析-质谱(TA-MS)联用系统中逸出气体质谱信号的定量,考察了多种实验参数如不同载气流速、温度以及分析样品量等因素对热分析-质谱联用系统中逸出气体质谱信号定量校正的影响.实验结果表明,利用PulseTA对TA-MS联用系统中逸出气体CO2定量结果与理论计算值的相对误差约2.85%.同时利用TG-DTG-MS联用技术对氮化铟(InN)粉体的热分解行为进行研究,在氩气气氛下InN粉体的热分解过程一步完成,InN粉体在550～750℃得到相应的正离子质谱峰:N2+(m/z=28),所释放的N非常接近InN中N的理论含量.利用PulseTA技术检测到InN粉体受热分解放出氮气质量的实验测量值与理论计算值的相对误差约为1.36%.     

蛋白质组学定量的技术与方法研究进展

蛋白质组学是一门在整体水平上研究细胞内蛋白质组成及其活动规律的新兴学科。定量蛋白质组学是指通过某种方法或技术，对生物样品(细胞、组织或体液等)在某些过程中蛋白质的含量进行比较分析。近几年来，定量蛋白质组的技术发展很快，稳定同位素标记技术的提出，为准确定量在细胞或组织体系中发挥重要功能的低丰度蛋白质提供了一个理想的方法。本文综述了蛋白质组定量分析技术及其最新的研究进展。     

Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC-MS for biomarker discovery

Label-free quantitative LC-MS profiling of complex body fluids has become an important analytical tool for biomarker and biological knowledge discovery in the past decade. Accurate processing, statistical analysis and validation of acquired data diversified by the different types of mass spectrometers, mass spectrometer parameter settings and applied sample preparation steps are essential to answer complex life science research questions and understand the molecular mechanism of disease onset and developments. This review provides insight into the main modules of label-free data processing pipelines with statistical analysis and validation and discusses recent developments. Special emphasis is devoted to quality control methods, performance assessment of complete workflows and algorithms of individual modules. Finally, the review discusses the current state and trends in high throughput data processing and analysis solutions for users with little bioinformatics knowledge.     

Ultra high performance liquid chromatography with quadrupole time-of-flight tandem mass spectrometry and liquid chromatography with tandem mass spectrometry combined with chemometric analysis as an approach for the quality evaluation of Mume Fructus

Mume Fructus is an important traditional Chinese medicine that has been widely used in the treatment of intestinal diseases and asthma for thousands of years. In order to evaluate the quality of Mume Fructus in different processing methods, the main chemical components in Mume Fructus were investigated and a method was established for simultaneous quantification of organic acids of Mume Fructus. First, an optimized ultra-performance liquid chromatography-quadrupole-time of flight tandem-mass spectrometry method was used to identify the structures of main components in Mume Fructus. A total of 41 chemical compounds were identified, including 11 organic acids, 13 flavonoids, and three fatty acids. The contents of 11 organic acids in 18 batches of Mume Fructus from different processing methods were simultaneously determined by a liquid chromatography with tandem mass spectrometry method. The results of quantitative and hierarchical cluster analysis indicated that Mume Fructus under different processing methods were rich in the above 11 organic acids and the contents were obviously different. Taken together, the proposed quality evaluation method was fast and comprehensively reflects the content of the main chemical components in Mume Fructus under different processing methods, and provides a useful reference for the quality control and evaluation of Mume Fructus.     

Quantitative densitometry from the point of view of information theory.

The process of quantitative densitometry is analyzed with methods developed in information theory. It is shown that the steps involved in densitometry, e.g. gel staining, mechanical, optical and electronic processing, as well as all the steps of data processing, can be viewed as communication channels. The factors affecting both the relevant and irrelevant part of the total information passed through these channels are discussed in the consistent frame provided by information theory. This view leads to a unifying context for analyzing the performance of quantitative densitometers.     

Data processing for mass spectrometry-based metabolomics

Modern analytical technologies afford comprehensive and quantitative investigation of a multitude of different metabolites. Typical metabolomic experiments can therefore produce large amounts of data. Handling such complex datasets is an important step that has big impact on extent and quality at which the metabolite identification and quantification can be made, and thus on the ultimate biological interpretation of results. Increasing interest in metabolomics thus led to resurgence of interest in related data processing. A wide variety of methods and software tools have been developed for metabolomics during recent years, and this trend is likely to continue. In this paper we overview the key steps of metabolomic data processing and focus on reviewing recent literature related to this topic, particularly on methods for handling data from liquid chromatography mass spectrometry (LC-MS) experiments.     

计算机辅助一清片径向展开薄层色谱定性与定量方法初探

径向薄层色谱法（RTLC）是一种将样品呈圆形或环状点样,然后将展开剂从中心向外沿径向输送的薄层色谱方法。在一定的展开距离内,RTLC是一种分离快速、扩散小、不拖尾的高效分离和半制备方法。目前关于RTLC分离的报道较多,但对RTLC定性和定量的报道较少。该文采用自编程方式结合图像处理软件,实现RTLC图像数字化处理,形成RTLC数字化图谱,并对RTLC进行定性与定量方法学验证,建立了一清片RTLC定性与定量方法。辅助计算机技术,对一清片径向展开薄层色谱定性与定量方法进行初探。结果表明,该方法用于RTLC定性的可靠度较好,但用于RTLC的定量,仍有不足之处,这可能与实验环境条件等有关。通过搭载更好的分离和数据采集设备,RTLC会有适合的用武之地。计算机图像处理和自编程方法的结合给了RTLC和其他一些分析相关的技术广阔的发展前景。相信未来在计算机技术的辅助下,薄层色谱技术会迈上一个新的台阶。     

Using additional standards for increasing the accuracy of quantitative chromatographic analysis

Uncontrolled partial losses at the step of sample injection into a gas chromatographic column increase errors of determination by the external standard, absolute calibration, and standard addition methods. Modified method is proposed for quantitative analysis; it includes the introduction of additional standards into test samples and calculations by the ratio between the areas of chromatographic peaks and peaks of standards rather than the absolute areas of chromatographic peaks. The calculation equations are presented for modified methods of quantitative analysis using additional standards, including those for estimating random errors of determination. The relative standard deviations of peak areas were shown to be 6–38-fold lower than the analogous statistical characteristics of absolute areas. This ensures a high accuracy of quantitative determinations even under the conditions of low reproducibility of sample dosing. Solvents contained in the analyzed samples can be used as additional standards. This version can be recommended as a routine method of data representation and processing.     

Non-selective chemical sensors in analytical chemistry: from “electronic nose” to “electronic tongue”

Development, recent historical background and analytical applications of promising sensor instruments based on sensor arrays with data processing by pattern recognition methods have been described. Attention is paid to the “electronic tongue” based on an array of original non-specific (non-selective) potentiometric chemical sensors. Application results for integral qualitative analysis of beverages and for quantitative analysis of biological liquids and solutions, containing heavy metals are reported. Discriminating abilities and precision obtained allow to consider “electronic tongue” as a perspective analytical tool.     

Use of household color-recording devices in quantitative chemical analysis

Published data on the use of household color-recording devices, such as office scanners, digital cameras, web cameras, mobile phones, and smartphones, in quantitative chemical analysis are generalized and systematized. The main approaches underlying the use of these devices for recording optical analytical signals are discussed. Methodological approaches used in the measurements and processing of the results are described. Examples of the determination of chemical compounds and ions using household color-recording devices are given.     

气相色谱质谱联用仪与微机的数据传输和处理

报道了一种用于气相色谱质谱联用仪和微机之间实现数据传输和处理的方法。方法可更有效地利用质谱仪采集的数据，解决了工作站处理数据的局限性。经数据格式转换，原始数据可以在微机上实现色谱峰再现，从而为色谱条件的优化和定量数据处理创造了条件。