Mass spectrometry combined with oxidative labeling for exploring protein structure and folding

This review discusses various mass spectrometry (MS)‐based approaches for exploring structural aspects of proteins in solution. Electrospray ionization (ESI)–MS, in particular, has found fascinating applications in this area. For example, when used in conjunction with solution‐phase hydrogen/deuterium exchange (HDX), ESI–MS is a highly sensitive tool for probing conformational dynamics. The main focus of this article is a technique that is complementary to HDX, that is, the covalent labeling of proteins by hydroxyl radicals. The reactivity of individual amino acid side chains with ^. OH is strongly affected by their degree of solvent exposure. Thus, analysis of the oxidative labeling pattern by peptide mapping and tandem mass spectrometry provides detailed structural information. A convenient method for ^. OH production is the photolysis of H₂O₂ by a pulsed UV laser, resulting in oxidative labeling on the microsecond time scale. Selected examples demonstrate the use of this technique for structural studies on membrane proteins, and the combination with rapid mixing devices for characterizing the properties of short‐lived protein (un)folding intermediates. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:651–667, 2010     

维A酸结合蛋白I折叠/伸展过程的氢/氘交换质谱研究

氢/氘交换质谱通过测定蛋白骨架中的氢（氘）与溶剂中氘（氢）的相互交换作用来研究蛋白的结构信息。采用氢/氘交换技术结合傅里叶变换离子回旋共振质谱研究氘代维A酸结合蛋白I与溶剂之间的氢/氘交换，发现在不同的pH值下，该蛋白的氢/氘交换具有不同的交换机理和交换速率，由其交换速率可估计不同交换时间蛋白骨架中残留的未交换的氢或氘的数目，确定蛋白骨架在溶剂中的暴露程度，得到蛋白的结构信息。     

非变性离子淌度质谱在蛋白质结构及构象疾病研究方面的应用

离子淌度质谱技术可以分离空间尺寸或构象不同的离子,能够在近似生理条件下表征蛋白质及其复合物的构象,可提供蛋白质及其复合物的构象稳定性及异质性、化学计量比等多重信息,已成为蛋白质构象及蛋白质-配体相互作用研究的重要手段。非变性离子淌度质谱还具有灵敏捕获蛋白质构象动态转变的特点,适用于低浓度、高异质性的蛋白混合物分析。本文综述了离子淌度质谱的基本原理、获取数据及信息形式、以及在蛋白质构象及蛋白质-配体相互作用研究领域的应用进展,重点关注其在蛋白质错误折叠、聚集动力学及与配体相互作用的应用研究。     

ICP‐MS‐Based strategies for protein quantification

In the post‐genomics era, proteomics has become a central branch in life sciences. An understanding of biological functions will not only rely on protein identification, but also on protein quantification in a living organism. Most of the existing methods for quantitative proteomics are based on isotope labeling combined with molecular mass spectrometry. Recently, a remarkable progress that utilizes inductively coupled plasma‐mass spectrometry (ICP‐MS) as an attractive complement to electrospray MS and MALDI MS for protein quantification, especially for absolute quantification, has been achieved. This review will selectively discuss the recent advances of ICP‐MS‐based technique, which will be expected to further mature and to become one of the key methods in quantitative proteomics. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:326–348, 2010     

Identification and characterization of molecular targets of natural products by mass spectrometry

Natural products, and their derivatives and mimics, have contributed to the development of important therapeutics to combat diseases such as infections and cancers over the past decades. The value of natural products to modern drug discovery is still considerable. However, its development is hampered by a lack of a mechanistic understanding of their molecular action, as opposed to the emerging molecule‐targeted therapeutics that are tailored to a specific protein target(s). Recent advances in the mass spectrometry‐based proteomic approaches have the potential to offer unprecedented insights into the molecular action of natural products. Chemical proteomics is established as an invaluable tool for the identification of protein targets of natural products. Small‐molecule affinity selection combined with mass spectrometry is a successful strategy to “fish” cellular targets from the entire proteome. Mass spectrometry‐based profiling of protein expression is also routinely employed to elucidate molecular pathways involved in the therapeutic and possible toxicological responses upon treatment with natural products. In addition, mass spectrometry is increasingly utilized to probe structural aspects of natural products–protein interactions. Limited proteolysis, photoaffinity labeling, and hydrogen/deuterium exchange in conjunction with mass spectrometry are sensitive and high‐throughput strategies that provide low‐resolution structural information of non‐covalent natural product–protein complexes. In this review, we provide an overview on the applications of mass spectrometry‐based techniques in the identification and characterization of natural product–protein interactions, and we describe how these applications might revolutionize natural product‐based drug discovery. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:126–155, 2010     

非变性结构质谱在蛋白提取、离子源开发与构象解析方面的研究进展

非变性条件下的蛋白质研究可以提供更准确的高级结构信息,为“序列-结构-功能”关系解析提供更接近生理条件的分子基础。非变性质谱(native MS)是在非变性条件下对目标蛋白质进行质谱分析的技术。近年来,非变性质谱在蛋白构象、蛋白质非共价相互作用以及蛋白质组装复合物等高阶结构解析中发挥着不可替代的作用,并逐渐成为结构生物学研究的重要支撑方法之一。本文总结了非变性结构质谱在蛋白提取、离子源开发与构象解析方面的发展现状,并提出了非变性结构质谱领域现阶段的技术瓶颈与潜在的解决策略,主要包含原位分析能力和结构分辨率的提升这两方面。     

The application of mass spectrometry in molecular dosimetry: Ethylene oxide as an example

Mass spectrometry plays an increasingly important role in the search for and quantification of novel chemically specific biomarkers. The revolutionary advances in mass spectrometry instrumentation and technology empower scientists to specifically analyze DNA and protein adducts, considered as molecular dosimeters, derived from reactions of a carcinogen or its active metabolites with DNA or protein. Analysis of the adducted DNA bases and proteins can elucidate the chemically reactive species of carcinogens in humans and can serve as risk‐associated biomarkers for early prediction of cancer risk. In this article, we review and compare the specificity, sensitivity, resolution, and ease‐of‐use of mass spectrometry methods developed to analyze ethylene oxide (EO)‐induced DNA and protein adducts, particularly N7‐(2‐hydroxyethyl)guanine (N7‐HEG) and N‐(2‐hydroxyethyl)valine (HEV), in human samples and in animal tissues. GC/ECNCI‐MS analysis after HPLC cleanup is the most sensitive method for quantification of N7‐HEG, but limited by the tedious sample preparation procedures. Excellent sensitivity and specificity in analysis of N7‐HEG can be achieved by LC/MS/MS analysis if the mobile phase, the inlet (split or splitless), and the collision energy are properly optimized. GC/ECNCI‐HRMS and GC/ECNCI‐MS/MS analysis of HEV achieves the best performance as compared with GC/ECNCI‐MS and GC/EI‐MS. In conclusion, future improvements in high‐throughput capabilities, detection sensitivity, and resolution of mass spectrometry will attract more scientists to identify and/or quantify novel molecular dosimeters or profiles of these biomarkers in toxicological and/or epidemiological studies. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:733–756, 2011     

Recent advances in mycotoxin determination in food and feed by hyphenated chromatographic techniques/mass spectrometry

Mycotoxins are fungal toxins produced by molds, which occur universally in food and feed derivatives, and are produced under certain environmental conditions in the field before harvest, post-harvest, during storage, processing, and feeding. Mycotoxin contamination is one of the most relevant and worrisome problem concerning food and feed safety because it can cause a variety of toxic acute and chronic effects in human and animals. In this review we report the use of mass spectrometry in connection with chromatographic techniques for mycotoxin determination by considering separately the most diffuse class of mycotoxins: patulin, aflatoxins, ochratoxin A, zearalenone, trichothecenes, and fumonisins. Although the selectivity of mass spectrometry is unchallenged if compared to common GC and LC detection methods, accuracy, precision, and sensitivity may be extremely variable concerning the different mycotoxins, matrices, and instruments. The sensitivity issue may be a real problem in the case of LC/MS, where the response can be very different for the different ionization techniques (ESI, APCI, APPI). Therefore, when other detection methods (such as fluorescence or UV absorbance) can be used for the quantitative determination, LC/MS appears to be only an outstanding confirmatory technique. In contrast, when the toxins are not volatile and do not bear suitable chromophores or fluorophores, LC/MS appears to be the unique method to perform quantitative and qualitative analyses without requiring any derivatization procedure. The problem of exact quantitative determination in GC/MS and LC/MS methods is particularly important for mycotoxin determination in food, given the high variability of the matrices, and can be solved only by the use of isotopically labeled internal standards or by the use of ionization interfaces able to lower matrix effects and ion suppressions. When the problems linked to inconstant ionization and matrix effects will be solved, only MS detectors will allow to simplify more and more the sample preparation procedures and to avoid clean-up procedures, making feasible low-cost, high-throughput determination of mycotoxins in many different food matrices.     

Tandem mass spectrometry in the study of fatty acids,bile acids,and steroids

Over the last 50 years, the mass spectrometry of lipids has evolved to become one of the most mature techniques in biomolecule analysis. Many volatile and non-polar lipids are directly amenable to analysis by gas-chromatography-mass spectrometry (GC-MS), a technique that combines the unsurpassed separation properties of gas-chromatography with the sensitivity and selectivity of electron ionization mass spectrometry. Less volatile and/or thermally labile lipids can be analyzed by GC-MS, following appropriate sample derivatization. However, many complex lipids are not readily analyzed by GC-MS, and it is these molecules that are the subject of the current review. Since the early 1970s, there have been three outstanding developments in mass spectrometry that are particularly appropriate in lipid analysis; i.e., the introduction of (i) fast atom bombardment (FAB); (ii) electrospray (ES); and (iii) tandem mass spectrometry (MS/MS). The FAB and ES ionization techniques will be discussed in relation to MS/MS, and examples of their application in biochemical studies will be presented. The review will concentrate on the analysis of fatty acids, bile acids, steroid conjugates, and neutral steroids.     

StructuralBiology:SomeStudiesbyMassSpectrometry

Traditionally, structural biology is studied using techniques such as X-ray crystallography and nuclear magnetic resonance (NMR). Both X-ray crystallography and NMR can solve structures with atomic resolution. Many biomolecules, however, cannot yield qualified crystals for X-ray crystallography, and NMR has limited application for very large biomolecules. Moreover, both techniques require relatively large amounts of samples that may be difficult to obtain in many cases. In recent years, mass spectrometry has emerged as a powerful tool for studies in structural biology, complementary to X-ray crystallography and NMR. In this talk, I would like to present some of our studies on protein complexes, using native mass spectrometry and hydrogen/deuterium exchange mass spectrometry. By using these approaches, we have been able to monitor the behaviour of protein complexes in solutions, to determine the stoichiometry, binding interfaces and conformational changes related to the protein interactions.     

Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples

Lipidomics, after genomics and proteomics, is a newly and rapidly expanding research field that studies cellular lipidomes and the organizational hierarchy of lipid and protein constituents mediating life processes. Lipidomics is greatly facilitated by recent advances in, and novel applications of, electrospray ionization mass spectrometry (ESI/MS). In this review, we will focus on the advances in ESI/MS, which have facilitated the development of shotgun lipidomics and the utility of intrasource separation as an enabling strategy for utilization of 2D mass spectrometry in shotgun lipidomics of biological samples. The principles and experimental details of the intrasource separation approach will be extensively discussed. Other ESI/MS approaches towards the quantitative analyses of global cellular lipidomes directly from crude lipid extracts of biological samples will also be reviewed and compared. Multiple examples of lipidomic analyses from crude lipid extracts employing these approaches will be given to show the power of ESI/MS techniques in lipidomics. Currently, modern society is plagued by the sequelae of lipid-related diseases. It is our hope that the integration of these advances in multiple disciplines will catalyze the development of lipidomics, and such development will lead to improvements in diagnostics and therapeutics, which will ultimately result in the extended longevity and an improved quality of life for humankind.     

Applications and advancements of FT-ICR-MS for interactome studies

The set of all intra- and intermolecular interactions, collectively known as the interactome, is currently an unmet challenge for any analytical method, but if measured, could provide unparalleled insight on molecular function in living systems. Developments and applications of chemical cross-linking and high-performance mass spectrometry technologies are beginning to reveal details on how proteins interact in cells and how protein conformations and interactions inside cells change with phenotype or during drug treatment or other perturbations. A major contributor to these advances is Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) technology and its implementation with accurate mass measurements on cross-linked peptide-pair precursor and fragment ions to enable improved identification methods. However, these applications place increased demands on mass spectrometer performance in terms of high-resolution spectral acquisition rates for on-line MSⁿ experiments. Moreover, FT-ICR-MS also offers unique opportunities to develop and implement parallel ICR cells for multiplexed signal acquisition and the potential to greatly advance accurate mass acquisition rates for interactome studies. This review highlights our efforts to exploit accurate mass FT-ICR-MS technologies with chemical cross-linking and developments being pursued to realize parallel MS array capabilities that will further advance visualization of the interactome.     

非变性质谱相关技术的研究进展

蛋白质与其他分子的相互作用几乎在所有的生命活动中起着核心调控作用,这些相互作用力和形成的蛋白质复合物是现代生命科学的研究重点。由于传统的生物物理技术对蛋白质复合物和相互作用的研究存在样品纯度要求高的限制,因此迫切需要新技术的出现,为结构生物学和相互作用组学的研究提供补充。质谱技术可以从原理上对混合样品进行检测,降低对样品纯度的要求,其中非变性质谱展现出强大的连接与互补作用。本文从样品制备、离子源、质量分析器、质谱联用技术等4方面介绍非变性质谱相关技术及近年来的研究进展,并总结分析未来面临的挑战以及发展方向。     

Measurement of mass flow rate and evaluation of heat transfer coefficient for high-pressure pneumatic components during charge and discharge processes

Both the mass flow rate and heat transfer characteristics are significant factors to the flow behavior of the high-pressure air; however, they are not easy to be obtained by analytical model during discharge and charge processes. In this paper, the mass flow rate characteristics of high-pressure pneumatic components (HPPC) are measured by a compounding approach; two components under test with the same geometry and dimension are needed to be connected in series. Both the effective cross-section area and critical pressure ratio of HPPC are determined accurately, and only the pressure variation and the steady-state temperature of air in the chamber are utilized. The compared results between experimental and simulation data show that the accuracy of the measured effective cross-section area and critical pressure ratio of the HPPC is high when the sonic and adiabatic releasing time is less than 2 s. And then, a new combined method of calculating the heat transfer coefficient during discharging and charging processes for the high-pressure air is proposed. The computational fluid dynamics (CFD) method is used to illustrate the intensity of heat exchange between the high-pressure air inside the chamber and outer atmosphere. The dynamic flow behavior is analyzed based on the tested flow rate characteristics of HPPC, mixed heat transfer theory and numerical results. The results show that the heat-transfer coefficient during charge process is much greater than discharge process, and the forced convection heat exchange happened owing to the strong “air agitation” during the charge process. The experimental results also validate that the proposed method of calculating the transient heat transfer coefficient is more reasonable to describe the heat transfer behavior. The findings may also have general implication in the development of the design and analysis of the high-pressure pneumatic system.     

Detection and localization of protein modifications by high resolution tandem mass spectrometry

For interrogation of peptides with diverse modifications, no other instrument is as versatile as the Fourier-transform mass spectrometer (FTMS). Particularly using electrospray ionization (ESI), many intact proteins and their proteolytic products harboring post-translational and chemical modifications (PTMs) have been studied by high resolution tandem mass spectrometry (MS/MS). The widely touted analytical figures of merit for FTMS in fact have translated into clarity when analyzing PTMs from phosphorylations to disulfides, oxidations, methylations, acetylations, and even exotic PTMs found in the biosynthesis of antibiotics and other natural products. A top down approach to PTM detection and localization is proving extensible to an increasing variety of PTMs, some of which are stable to MS/MS at the protein level but unstable to amide bond cleavage by threshold dissociations at the level of small peptides <3 kDa. In contrast, MS/MS using electron capture dissociation (ECD) allows precise localization of even labile PTMs given enough sample and abundant molecular ions. Finally, this brief synopsis of recent literature highlights specific PTMs that perturb the protein backbone therefore altering MS/MS fragmentation patterns. Thus, FTMS will continue its expansion into more laboratories in part because of its ability to detect and deconvolute the regulatory mechanisms of biology written in the language of PTMs.     

Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry

Photochemical cross-linking is a commonly used method for studying the molecular details of protein-nucleic acid interactions. Photochemical cross-linking aids in defining nucleic acid binding sites of proteins via subsequent identification of cross-linked protein domains and amino acid residues. Mass spectrometry (MS) has emerged as a sensitive and efficient analytical technique for determination of such cross-linking sites in proteins. The present review of the field describes a number of MS-based approaches for the characterization of cross-linked protein-nucleic acid complexes and for sequencing of peptide-nucleic acid heteroconjugates. The combination of photochemical cross-linking and MS provides a fast screening method to gain insights into the overall structure and formation of protein-oligonucleotide complexes. Because the analytical methods are continuously refined and protein structural data are rapidly accumulating in databases, we envision that many protein-nucleic acid assemblies will be initially characterized by combinations of cross-linking methods, MS, and computational molecular modeling.     

A multi-angular mass spectrometric view at cyclic nucleotide dependent protein kinases: in vivo characterization and structure/function relationships

Mass spectrometry has evolved in recent years to a well-accepted and increasingly important complementary technique in molecular and structural biology. Here we review the many contributions mass spectrometry based studies have made in recent years in our understanding of the important cyclic nucleotide activated protein kinase A (PKA) and protein kinase G (PKG). We both describe the characterization of kinase isozymes, substrate phosphorylation, binding partners and post-translational modifications by proteomics based methodologies as well as their structural and functional properties as revealed by native mass spectrometry, H/D exchange MS and ion mobility. Combining all these mass spectrometry based data with other biophysical and biochemical data has been of great help to unravel the intricate regulation of kinase function in the cell in all its magnificent complexity.