生物质谱分析的研究进展及临床应用

质谱分析技术已应用于化学、化工、环境、能源、医药、运动医学、刑侦科学、生命科学、材料科学等各个领域。阐述目前生物质谱技术的类型、原理以及在医学领域中的应用,进而分析质谱技术在未来发展的前景。     

质谱技术解析磷酸化蛋白质组

蛋白质磷酸化是生物体内存在的一种普遍的调节方式,在细胞信号传递中占有极重要的地位.质谱已逐渐被人们认为是挑战这一领域的有利工具.综述了目前利用质谱技术分析磷酸化蛋白质的方法,包括利用固定化的金属亲和层析柱、抗体和化学标签技术富集目的分子,肽片段质量图和前体离子扫描（precusor ion scans）等技术检测磷酸化肽段,串联质谱对磷酸化肽段测序鉴定磷酸化位点,以及引入质量标签对蛋白质的磷酸化水平进行定量等.虽然现在已经有很多可行的方法用于分析磷酸化蛋白质,但要达到从少量生物样品中解析其全部磷酸化蛋白质仍需要有很多技术上的突破.     

基于质谱技术的神经肽研究进展

神经肽是一类重要的内源活性物质,在神经系统中发挥重要的作用,并连接大脑和其他神经器官。基于质谱技术的神经肽组学研究旨在对神经肽进行大规模研究,在分子水平上得到重要信息,进一步加深对神经系统调控机制以及神经疾病致病机理的理解。文中综述了利用质谱技术进行神经肽研究的基本策略,包括样品处理、定性定量方法以及质谱成像等研究进展。     

环烯醚萜甙的快速原子轰击质谱和场解吸质谱研究

环烯醚萜甙是植物界分布较广泛的一类配糖体成分,极性较大,用通常的电子轰击质谱测试不能得到分子离子信息,且离子碎片零碎,难以进行结构解析。本文对２５个不同类型的环烯醚萜甙进行正,负离子快速原子轰击质谱和场解吸质谱分析,并讨论这两种质谱新技术在环烯醚萜甙类化合物结构解析中的应用。     

生物质谱技术在糖蛋白结构分析中的应用

生物质谱包括基质辅助激光解吸附飞行时间质谱及电喷雾质谱被广泛应用于生物样品如多肽、蛋白质及核酸的分析,由于这种具有软电离方式的质谱具有极高的灵敏度及准确度,目前也被成功地用于糖蛋白的结构分析,与普通的化学方法相比,质谱法快速、简单,结合网上数据库检索、凝集素亲和提取、二维凝胶电泳以及靶上直接酶切等新方法,可以提供糖蛋白的一级结构乃至高级结构的信息。     

质谱图聚类网络法在鉴定多肽翻译后修饰中的应用及研究进展

蛋白质组学多肽鉴定方法一直以基于质谱分析和数据库搜索的方法为主,随着质谱仪技术的发展,海量的质谱数据被获取,这为大规模蛋白质的鉴定提供了一个强大的数据仓库,使得以质谱数据为基础的蛋白质组学研究成为主流。传统的串联质谱图搜库方法鉴定多肽翻译后修饰时具有诸多局限,质谱网络方法可以在一定程度上弥补局限。文中系统综述了基于质谱聚类的质谱网络和质谱图库搜索方法的发展历程、理论研究和应用研究,讨论了质谱网络库方法在鉴定多肽翻译后修饰的优势,并进行了分析和展望。     

综述: 基于质谱技术的糖链结构解析研究进展

糖组学是继基因组学、蛋白质组学之后,又一门新兴的学科,其主要是研究糖分子的结构与功能．糖是一类比核酸、蛋白质更加独特的生物分子,它们不仅是生物体储存能量和释放能量的主要物质,更是生物体内的信息传递分子,并且在生理和病理过程中扮演着重要的角色,如细胞间的识别作用、炎症以及自身免疫疾病等．在结构上,糖类物质更为复杂,具有宏观不均一性(蛋白质上有多个糖基化位点)和微观不均一性(同一结合位点上可以连接不同的多糖),所以糖链的结构解析一直是糖组学研究的难题．相较于传统的分析方法,质谱法具有高灵敏度、高精度、高通量等优势,被认为是在糖链结构解析过程中重要的分析方法．本文综述了质谱、多级质谱、液相色谱-质谱、毛细管电泳-质谱等方法在糖组学中糖链结构解析的研究进展．     

水稻蛋白质组学研究

水稻是全球最重要的粮食作物之一,目前水稻基因组精细图谱已得到全面解析,运用以双向电泳和质谱分析为主的蛋白质组技术平台对水稻各种组织器官进行蛋白质组学研究也取得了诸多进展,对水稻蛋白质组研究背景,技术路线及取得的进展进行了介绍,并对水稻蛋白质组的发展作了展望。     

化学交联质谱技术的研究进展

化学交联质谱技术是解析蛋白质结构和研究蛋白质相互作用的重要工具。近5年以来,该技术在方法和应用上都取得了很大的进步。方法上,一方面可断裂交联剂与新型分离富集方法展现了较好的应用前景,另一方面更加高效的交联肽段搜索引擎和质量控制方法为交联质谱数据分析提供了有力的工具。应用上,一方面与冷冻电镜技术结合解析了大量蛋白质的结构,另一方面从研究蛋白质复合物的相互作用发展到研究全蛋白质组水平的相互作用网络。化学交联质谱技术在方法和应用上的蓬勃发展,体现了这一技术的重要作用。本文对化学交联质谱技术的各个环节进行了详细的综述,包括交联剂选择、交联反应、酶切、交联肽段富集、液质联用、交联肽段鉴定、质量控制和生物学应用,重点介绍了最近5年的研究进展。最后,讨论了化学交联质谱技术面临的挑战及未来的发展方向。     

气相色谱—质谱联用技术在植物激素分析中的应用

本文结合自己多年来工作的体会介绍了GC—MS技术如何用于植物激素分析和在分析过程中应注意的关键技术问题。     

Identifying new PCR targets for pathogenic bacteria using top-down LC/MS protein discovery.

We have investigated the use of a top-down liquid chromatography/mass spectrometric (LC/MS) approach for the identification of specific protein biomarkers useful for differentiation of closely related strains of bacteria. The sequence information derived from the protein biomarker was then used to develop specific polymerase chain reaction primers useful for rapid identification of the strains. Shiga-toxigenic Escherichia coli (STEC) strains were used for this evaluation. The expressed protein profiles of two closely related serotype 0157:H7 strains, the predominant strain implicated in illness worldwide, and the nonpathogenic E. coli K-12 strain were compared with each other in an attempt to identify new protein markers that could be used to distinguish the 0157:H7 strains from each other and from the E. coli K-12 strain. Sequencing of a single protein unique to one of the 0157:H7 strains identified it as a cytolethal distending toxin, a potential virulence marker. The protein sequence information enabled the derivation of genetic sequence information for this toxin, thus allowing the development of specific polymerase chain reaction primers for its detection. In addition, the top-down LC/MS technique was able to identify other unique biomarkers and differentiate nearly identical 0157:H7 strains, which exhibited identical phenotypic, serologic, and genetic traits. The results of these studies demonstrate that this approach can be expanded to other serotypes of interest and provide a rational approach to identifying new molecular targets for detection.     

Accessing the reproducibility and specificity of pepsin and other aspartic proteases

The aspartic protease pepsin is less specific than other endoproteinases. Because aspartic proteases like pepsin are active at low pH, they are utilized in hydrogen deuterium exchange mass spectrometry (HDX MS) experiments for digestion under hydrogen exchange quench conditions. We investigated the reproducibility, both qualitatively and quantitatively, of online and offline pepsin digestion to understand the compliment of reproducible pepsin fragments that can be expected during a typical pepsin digestion. The collection of reproducible peptides was identified from > 30 replicate digestions of the same protein and it was found that the number of reproducible peptides produced during pepsin digestion becomes constant above 5–6 replicate digestions. We also investigated a new aspartic protease from the stomach of the rice field eel (Monopterus albus Zuiew) and compared digestion efficiency and specificity to porcine pepsin and aspergillopepsin. Unique cleavage specificity was found for rice field eel pepsin at arginine, asparagine, and glycine. Different peptides produced by the various proteases can enhance protein sequence coverage and improve the spatial resolution of HDX MS data. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.     

Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics

Recent developments in combined separations with mass spectrometry for sensitive and high-throughput proteomic analyses are reviewed herein. These developments primarily involve high-efficiency (separation peak capacities of ~10³) nanoscale liquid chromatography (flow rates extending down to approximately 20 nl/min at optimal liquid mobile-phase separation linear velocities through narrow packed capillaries) in combination with advanced mass spectrometry and in particular, high-sensitivity and high-resolution Fourier transform ion cyclotron resonance mass spectrometry. Such approaches enable analysis of low nanogram level proteomic samples (i.e., nanoscale proteomics) with individual protein identification sensitivity at the low zeptomole level. The resultant protein measurement dynamic range can approach 10⁶ for nanogram-sized proteomic samples, while more abundant proteins can be detected from subpicogram-sized (total) proteome samples. These qualities provide the foundation for proteomics studies of single or small populations of cells. The instrumental robustness required for automation and providing high-quality routine performance nanoscale proteomic analyses is also discussed.     

A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra

A novel hierarchical MS²/MS³ database search algorithm has been developed to analyze MS²/MS³ phosphopeptides proteomic data. The algorithm is incorporated in an automated database search program, MassMatrix. The algorithm matches experimental MS² spectra against a supplied protein database to determine candidate peptide matches. It then matches the corresponding experimental MS³ spectra against those candidate peptide matches. The MS² and MS³ spectra are used in concert to arrive at peptide matches with overall higher confidence rather than combining MS² and MS³ data searched separately. Receiver operating characteristic analysis showed that hierarchical MS²/MS³ database searches with MassMatrix had better sensitivity and specificity than the two‐stage MS²/MS³ database searches obtained with MassMatrix, MASCOT, and X!Tandem. A greater number of true peptide matches at a given false rate were identified by use of this new algorithm for data collected on both LCQ and LTQ‐FTICR mass spectrometers. The additional MS³ spectral data also improved the overall reliability and the number of true positives (TPs) due to the fact that the TPs of the MS²/MS³ search results had higher scores than those of the MS².     

Characterization of pII family (GlnK1, GlnK2, and GlnB) protein uridylylation in response to nitrogen availability for Rhodopseudomonas palustris

The GlnK and GlnB proteins are members of the pII signal transduction protein family, which is essential in nitrogen regulation due to this protein family's ability to sense internal cellular ammonium levels and control cellular response. The role of GlnK in nitrogen regulation has been studied in a variety of bacteria but previously has been uncharacterized in the purple nonsulfur anoxygenic phototropic bacterium Rhodopseudomonas palustris. R. palustris has tremendous metabolic versatility in its modes of energy generation and carbon metabolism, and it employs a sensitive nitrogen-ammonium regulation system that may vary from that of other commonly studied bacteria. In R. palustris, there are three annotated forms of pII proteins: GlnK1, GlnK2, and GlnB. Here we describe, for the first time, the characterization of GlnK1, GlnK2, and GlnB modifications as a response to nitrogen availability, thereby providing information about how this bacterium regulates the AmtB ammonium transporter and glutamine synthetase, which controls the rate of glutamate to glutamine conversion. Using a strategy of creating C-terminally tagged GlnK and GlnB proteins followed by tandem affinity purification in combination with top-down mass spectrometry, four isoforms of the GlnK2 and GlnB proteins and two isoforms of the GlnK1 protein were characterized at high resolution and mass accuracy. Wild-type or endogenous expression of all three proteins was also examined under normal ammonium conditions and ammonium starvation to ensure that the tagging and affinity purification methods employed did not alter the natural state of the proteins. All three proteins were found to undergo uridylylation under ammonium starvation conditions, presumably to regulate the AmtB ammonium transporter and glutamine synthetase. Under high-ammonium conditions, the GlnK1, GlnK2, and GlnB proteins are unmodified. This experimental protocol involving high-resolution mass spectrometry measurements of intact proteins provides a powerful method of examining the posttranslational modifications that play a crucial role in both the regulation of the AmtB ammonium transporter and glutamine synthetase within R. palustris.     

A fast and simple assay for busulfan in serum or plasma by liquid chromatography-tandem mass spectrometry using turbulent flow online extraction technology

Busulfan is used in myeloablative preparation regimens for hematopoietic bone marrow transplantation. Due to its narrow therapeutic range therapeutic drug monitoring of busulfan is recommended. In this study a fast and simple method for measuring busulfan in serum or plasma by liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been developed utilizing turbulent flow online extraction technology. Serum or plasma was mixed with acetonitrile containing d(8)-busulfan. After centrifugation the supernatant was injected onto a turbulent flow preparatory column then transferred to a C18 analytical column monitored by a tandem mass spectrometer set at positive electrospray ionization. The analytical cycle time was 4.0min. The method was linear from 0.15 to 41.90μmol/L with an accuracy of 87.9-103.0%. Inter- and intra-assay CVs across four concentration levels were 2.1-7.8%. No significant carryover or ion suppression was observed. No interference was observed from commercial control materials containing more than 100 compounds. Comparison with a well established LC-MS/MS method using patient specimens (n=45) showed a mean bias 1.3% with Deming regression of slope 1.02, intercept -0.02μmol/L, and a linear correlation coefficient 0.9883. The LC-MS/MS method coupled with turbulent flow online sample cleaning technology described here offers reliable busulfan quantitation in serum or plasma with minimum manual sample preparation and was fully validated for clinical use.     

Automated Protein Preparation Techniques Using a Digest Robot

Since the introduction of fast analysis methods for peptide mixtures such as MALDI-MS, peptide micropreparation and digest methods have become an important bottleneck in the protein characterization process. We therefore developed and describe here a digest robot capable of processing 30 protein samples in parallel [Houthaeve el al. (1995), FEBS Lett. 376, 91–94]. Briefly, after gel pieces or blots are cut out, they are loaded in flowthrough reactors and these are loaded in a thermocontrolled reactor block. The proteins are then washed, reduced, and alkylated, proteolytically or chemically cleaved, and resulting peptides extracted. The system allows the parallel use of different reagents and enzymes during the same run, and is compatible with RP-HPLC peptide separation and Edman degradation, MALDI-MS, and NanoES-MS/MS. The digest robot is now also commercially available from ABIMED. In an ongoing project aimed at elucidating proteinaceous structures involved in the functional and structural maintenance of the Golgi apparatus, we illustrate the strength of the digest robot for the fast analysis of several proteins. We conclude that the performance of the digest robot is comparable to currently used manual digestion methods. The approach outlined makes sample preparation procedures faster, simpler, and less labor-intensive.     

Mass spectrometric approaches for characterizing bacterial proteomes

The emergence of advanced liquid chromatography mass spectrometry technologies for characterizing very complex mixtures of proteins has greatly propelled the field of proteomics, the goal of which is the simultaneous examination of all the proteins expressed by an organism. This research area represents a paradigm shift in molecular biology by attempting to provide a top-down qualitative and quantitative view of all the proteins (including their modifications and interactions) that are essential for an organism’s life cycle, rather than targeting a particular protein family. This level of global protein information about an organism such as a bacterium can be combined with genomic and metabolomic data to enable a systems biology approach for understanding how these organisms live and function.     

Oxidation-sensitive residues mediate the DNA bending abilities of the architectural MC1 protein

The Methanosarcina thermophila MC1 protein is a small basic protein that is able to bend DNA sharply. When this protein is submitted to oxidative stress through gamma irradiation, it loses its original DNA interaction properties. The protein can still bind DNA but its ability to bend DNA is decreased dramatically. Here, we used different approaches to determine the oxidations that are responsible for this inactivation. Through a combination of proteolysis and mass spectrometry we have identified the three residues that are oxidized preferentially. We show by site directed mutagenesis that two of these residues, Trp74 and Met75, are involved in the DNA binding. Their substitution by alanine leads to a strong reduction in the protein capacity to bend DNA, and a total loss of its ability to recognize bent DNA. Taken together, these results show that oxidation of both these residues is responsible for the protein inactivation. Furthermore, the results confirm the strong relationship between DNA bending and recognition of DNA sequences by the MC1 protein.