Identification of protein associations in organelles, using mass spectrometry-based proteomics

Recent literature that highlights the power of using mass spectrometry (MS) for protein identification from preparations of highly purified organelles and other large subcellular structures is covered in this review with an emphasis on techniques that preserve the integrity of the functional protein complexes. Recent advances in distinguishing contaminant proteins from "bonafide" organelle-localized proteins and the affinity capture of protein complexes are reviewed, as well as bioinformatic strategies to predict protein organellar localization and to integrate protein-protein interaction maps obtained from MS-affinity capture methods with data obtained from other techniques. Those developments demonstrate that a revolution in cellular biology, fueled by technical advances in MS-based proteomic techniques, is well underway.     

Subcellular phosphoproteomics

Protein phosphorylation represents one of the most extensively studied post‐translational modifications, primarily due to the emergence of sensitive methods enabling the detection of this modification both in vitro and in vivo. The availability of enrichment methods combined with sensitive mass spectrometry instrumentation has played a crucial role in uncovering the dynamic changes and the large expanding repertoire of this reversible modification. The structural changes imparted by the phosphorylation of specific residues afford exquisite mechanisms for the regulation of protein functions by modulating new binding sites on scaffold proteins or by abrogating protein–protein interactions. However, the dynamic interplay of protein phosphorylation is not occurring randomly within the cell but is rather finely orchestrated by specific kinases and phosphatases that are unevenly distributed across subcellular compartments. This spatial separation not only regulates protein phosphorylation but can also control the activity of other enzymes and the transfer of other post‐translational modifications. While numerous large‐scale phosphoproteomics studies highlighted the extent and diversity of phosphoproteins present in total cell lysates, the further understanding of their regulation and biological activities require a spatio‐temporal resolution only achievable through subcellular fractionation. This review presents a first account of the emerging field of subcellular phosphoproteomics where cell fractionation approaches are combined with sensitive mass spectrometry methods to facilitate the identification of low abundance proteins and to unravel the intricate regulation of protein phosphorylation. © 2010 Wiley Periodicals, Inc. Mass Spec Rev 29:962–990, 2010     

Ultrastructural localization of prion proteins: physiological and pathological implications

The transmissible spongiform encephalopathies (TSE) or prion diseases are fatal neurodegenerative disorders in which the central event is the conversion of a normal host-encoded protein (PrP(c)) into an abnormal isoform (PrP(sc)) which accumulates as amyloid in TSE brain. The two PrP(c) and PrP(sc) prion protein isoforms are membrane sialoglycoproteins synthesized in the central nervous system and various peripheral organ tissues. In this review, we describe the ultrastructural localization of prion proteins in human and animal cerebral and non-cerebral tissues whether or not infected by TSE agents. In addition to the plasma membrane of several cells, PrP(c) was found in association with cytoplasmic organelles of central and nerve-muscle synapses, and secretory granules of epithelial cells. Fibrils of amyloid plaques, synaptic structures, and lysosome-like organelles constitute the subcellular sites harboring PrP(sc). These findings have led to discussions on the physiological role of PrP(c) and the pathological mechanisms underlying prion spongiform encephalopathies.     

Fluorescent proteins as markers in the plant secretory pathway

The use of fluorescent proteins and live cell imaging has greatly increased our knowledge of cell biology in recent years. Not only can these technologies be used to study protein trafficking under different conditions, but they have also been of use in elucidating the relationships between different organelles in a noninvasive manner. The use of multiple different fluorochromes allows the observation of interactions between organelles and between proteins, making this one of the fastest-developing and exciting fields at this time. In this review, we discuss the multitude of fluorescent markers that have been generated to study the plant secretory pathway. Although these markers have been used to solve many mysteries in this field, some areas that require further discussion remain.     

Localization of membrane-bound and soluble antigens using peroxidase-labeled antibodies and preembedding immunoelectron microscopy

The immunoelectron microscopy preembedding method using peroxidase-labeled antibodies has enabled us to localize various bioactive substances in subcellular organelles, i.e., nucleus, cytosol, perinuclear space, rough endoplasmic reticulum, Golgi complex, secretory granules, mitochondria, etc. In this text, detailed procedures and some key points for the appropriate staining are described. The applications of this technique to localize substances in various organelles and to observe ultrastructural changes of intracellular hormones are also discussed.     

Mass spectrometry and the search for moonlighting proteins

Mass spectrometry has become one of the most important techniques in proteomics because of its use to identify the proteins found in different cell types, organelles, and multiprotein complexes. This information about protein location and binding partners can provide valuable clues to infer a protein's function. However, more and more proteins are found that "moonlight," or have more than one function, and the presence of moonlighting proteins can make more difficult the identification of protein function in those studies. This review discusses examples of moonlighting proteins and how their presence can affect the results of mass spectrometry studies that identify the locations, levels, and changes in protein expression. Although the presence of moonlighting proteins can complicate the results of those studies, mass spectrometry-derived protein-expression profiles potentially provides a very powerful method to find additional moonlighting proteins because they do not require a prior hypothesis of the protein's function.     

A review of current applications of mass spectrometry for neuroproteomics in epilepsy

The brain is unquestionably the most fascinating organ, and the hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In temporal lobe epilepsy (TLE), the seizure origin typically involves the hippocampal formation. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward an improved understanding of the complex molecular mechanisms that underlie functions of the brain and hippocampus is neuroproteomics. Mass spectrometry has been widely used to analyze biological samples, and has evolved into an indispensable tool for proteomics research. In this review, we present a general overview of the application of mass spectrometry in proteomics, summarize neuroproteomics and systems biology‐based discovery of protein biomarkers for epilepsy, discuss the methodology needed to explore the epileptic hippocampus proteome, and also focus on applications of ingenuity pathway analysis (IPA) in disease research. This neuroproteomics survey presents a framework for large‐scale protein research in epilepsy that can be applied for immediate epileptic biomarker discovery and the far‐reaching systems biology understanding of the protein regulatory networks. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of epilepsy on society. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:197–246, 2010     

质谱多反应监测技术（MRM）及其在蛋白质细胞器定位与定量研究中的应用

肝脏中的蛋白质只有处于特定的亚细胞中才能发挥其功能。研究特定蛋白质的亚细胞定位对于肝脏功能研究有重要意义[1]。对于多定位的蛋白质,确定其在不同细胞器中量的变化,也是肝脏蛋白表达谱研究的重要内容之一。目前,蛋白亚细胞定位分析方法主要包括实验方法和理论预测方法两大类。其中实验方法主要有绿色荧光蛋白（GFP）-激光共聚焦显微镜法、免疫电镜胶体金标记法、差速离心-免疫印迹法等。理论预测方法主要根据蛋白质的氨基酸组成、氨基酸对组成以及位置特异性打分矩阵等分类特征,采用模糊k近邻、支持向量机及分组重量编码法等方法进行理论预测。实验方法不仅分析通量低,还需要特异的抗体,并且在定位的同时难以实现定量分析。对于不同的理论预测方法而言,往往会得出不同的结论,准确度差。因而需要建立一种可以实现通量化、准确地进行蛋白亚细胞定位及定量分析的方法。 近年来,质谱多反应监测技术（MRM）在蛋白质定量分析方面的应用越来越广泛^[2]。该技术通过特异性的检测预先设置的母离子和子离子,在母离子和子离子两个水平排除其它离子的检测干扰, 从而增强检测的特异性。同时结合同位素稀释技术可以同时实现对多种目标蛋白质的绝对定量。由于该技术采用特异性检测预设的母子离子对的方法,从而保证了检测的重现性。而依据特定子离子和相应的同位素标记子离子对峰面积进行绝对定量的方法保证了定量的可靠性。同时可以批量化同时进行多个蛋白质的亚细胞定量及定位分析。因而本研究利用MRM技术,用于目标蛋白在肝脏细胞器中定位及定量分析研究。 鉴于本研究样品采用蔗糖密度梯度离心法制备,首先对细胞器样品的分离效果进行评价。选用文献报道^[3]的正向和反向免疫评价抗体蛋白,包括线粒体Marker蛋白COX4、VDAC和Cytc,细胞核Marker蛋白Lamin B,质膜Marker蛋白Na＋K＋-ATPase等。利用MRM技术分析蛋白在不同细胞器样品中的含量,从而对细胞器样品纯度进行评价。同时考察方法的灵敏度,重现性以及动态范围。 在确定了细胞器样品纯度的基础上,利用MRM质谱技术对选定的部分目标蛋白进行了定位分析。根据这些蛋白在不同细胞器样品中的含量,判断其在不同细胞器样品中的定位。并选择其中一些蛋白进行GFP-激光共聚焦显微镜分析,与基于MRM技术的定位分析结果进行对比验证。     

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     

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     

Secretory vesicles in live cells are not free-floating but tethered to filamentous structures: a study using photonic force microscopy

It is well established that actin and microtubule cytoskeletal systems are involved in organelle transport and membrane trafficking in cells. This is also true for the transport of secretory vesicles in neuroendocrine cells and neurons. It was however unclear whether secretory vesicles remain free-floating, only to associate with such cytoskeletal systems when needing transport. This hypothesis was tested using live pancreatic acinar cells in physiological buffer solutions, using the photonic force microscope (PFM). When membrane-bound secretory vesicles (0.2-1.2 microm in diameter) in live pancreatic acinar cells were trapped at the laser focus of the PFM and pulled, they were all found tethered to filamentous structures. Mild exposure of cells to nocodazole and cytochalasin B, disrupts the tether. Immunoblot analysis of isolated secretory vesicles, further demonstrated the association of actin, myosin V, and kinesin. These studies demonstrate for the first time that secretory vesicles in live pancreatic acinar cells are tethered and not free-floating, suggesting that following vesicle biogenesis, they are placed on their own railroad track, ready to be transported to their final destination within the cell when required. This makes sense, since precision and regulation are the hallmarks of all cellular process, and therefore would hold true for the transport and localization of subcellular organelles such as secretory vesicles.     

A quantitative interference light microscope study of human first trimester chorionic villi

Using a Jamin-Lebedeff-type interference microscope an analysis of frozen sections of human first trimester chorionic villi reveals regional differences down to subcellular resolution. The evidence indicates compositional differences between villus cell types and shows that the syncytiotrophoblast is differentiated into at least three layers, one of which corresponds positionally to the previously described syncytioskeletal layer. Quantitative measurements have been made of specimen thickness, refractive index and dry mass of regions in the tissue. Local differences in syncytiotrophoblast have been noted with respect to the content of a population of organelles with distinctive optical properties. These may correspond to stored forms of steroid hormone or their precursors.     

Power and limitations of electrophoretic separations in proteomics strategies

Proteomics can be defined as the large‐scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 28:816–843, 2009     

An automated tracking system to measure the dynamic properties of vesicles in living cells

Recent technological improvements have made it possible to examine the dynamics of individual vesicles at a very high temporal and spatial resolution. Quantification of the dynamic properties of secretory vesicles is labor-intensive and therefore it is crucial to develop software to automate the process of analyzing vesicle dynamics. Dual-threshold and binary image conversion were applied to enhance images and define the areas of objects of interest that were to be tracked. The movements, changes in fluorescence intensity, and changes in the area of each tracked object were measured using a new software system named the Protein Tracking system (PTrack). Simulations revealed that the system accurately recognized tracked objects and measured their dynamic properties. Comparison of the results from tracking real time-lapsed images manually with those automatically obtained using PTrack revealed similar patterns for changes in fluorescence intensity and a high accuracy (<89%). According to tracking results, PTrack can distinguish different vesicular organelles that are similar in shape, based on their unique dynamic properties. In conclusion, the novel tracking system, PTrack, should facilitate automated quantification of the dynamic properties of vesicles that are important when classifying vesicular protein locations.     

The application of quantification techniques in proteomics for biomedical research

The systematic analysis of biological processes requires an understanding of the quantitative expression patterns of proteins, their interacting partners and their subcellular localization. This information was formerly difficult to accrue as the relative quantification of proteins relied on antibody‐based methods and other approaches with low throughput. The advent of soft ionization techniques in mass spectrometry plus advances in separation technologies has aligned protein systems biology with messenger RNA, DNA, and microarray technologies to provide data on systems as opposed to singular protein entities. Another aspect of quantitative proteomics that increases its importance for the coming few years is the significant technical developments underway both for high pressure liquid chromatography and mass spectrum devices. Hence, robustness, reproducibility and mass accuracy are still improving with every new generation of instruments. Nonetheless, the methods employed require validation and comparison to design fit for purpose experiments in advanced protein analyses. This review considers the newly developed systematic protein investigation methods and their value from the standpoint that relative or absolute protein quantification is required de rigueur in biomedical research. © 2012 Wiley Periodicals, Inc., Mass Spec Rev 32:1–26, 2013     

Glycomic analysis by capillary electrophoresis-mass spectrometry

The occurrence of multiple glycosylation sites on a protein, together with the number of glycan structures which could potentially be associated with each site (microheterogeneity) often leads to a large number of structural combinations. These structural variations increase with the molecular size of a protein, thus contributing to the complexity of glycosylation patterns. Resolving such fine structural differences has been instrumentally difficult. The degree of glycoprotein microheterogeneity has been analytically challenging in the identification of unique glycan structures that can be crucial to a distinct biological function. Despite the wealth of information provided by the most powerful mass spectrometric (MS) and tandem MS techniques, they are not able to readily identify isomeric structures. Although various separation methods provide alternatives for the analysis of glycan pools containing isomeric structures, capillary electrophoresis (CE) is often the method of choice for resolving closely related glycan structures because of its unmatched separation efficiency. It is thus natural to consider combining CE with the MS-based technologies. This review describes the utility of different CE approaches in the structural characterization of glycoproteins, and discusses the feasibility of their interface to mass spectrometry.     

Recent advances in mass spectrometry analysis of phenolic endocrine disruptors and related compounds

This article reviews recent literature on current methodologies based on chromatography coupled to mass spectrometry to analyze phenolic compounds with endocrine‐disrupting capabilities. For this review we chose alkylphenol ethoxylates, bisphenol A, bisphenol F, and their degradation products and halogenated derivatives, which are considered important environmental contaminants. Additionally, some related compounds such as bisphenol diglycidylethers were included. Growing attention has been paid to the mass spectrometric characterization of these compounds and the instrumentation and strategies used for their quantification and confirmation. The current use of gas chromatography–mass spectrometry (GC–MS) and liquid chromatography–mass spectrometry (LC–MS) methodologies with different mass spectrometers and ionization and monitoring modes is discussed. Practical aspects with regards to the use of these analytical techniques, such as derivatizing reagents in GC–MS, ion suppression in LC–MS, and the most problematic aspects of quantification, are included in the discussion. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:776–805, 2010     

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。     

The cytoskeleton in fish melanophore melanosome positioning

Melanophore melanosomes organelles can be regulated to move and locate correspondingly to many other different organelle types. Comparing lessons from analysis of a specific melanosome distribution can, therefore, contribute to the understanding of distribution of other organelles, and vice versa. From such data, it is now generally accepted that microtubules provide directed long-distance movement, while cell peripheral movements include microfilaments. In fish melanophores, both actin and dynein exhibit counter-forces to the kinesin-like protein in maintaining the evenly dispersed state, while actin and kinesin exhibit counter-forces to dynein in many other systems. Lessons from elevating cAMP levels indicate the presence of a peripheral feedback regulatory system involved in maintaining the evenly dispersed state. Studies from dynein inhibition suggest that the kinesin-like protein involved in fish melanosome dispersal is regulated in contrast to many other systems. One would further expect melanosome transport to be regulated also on actin/myosin, in order to prevent actin-dependent capture of melanosomes during the microtubule-dependent aggregation and dispersion. General findings will be discussed in comparison with positioning and movement of other organelle types in cells. Finally, recent data on melanosome-dependent organising of microtubules show that dynein is involved in nucleating microtubules extending from melanosome aggregates in melanophore fragments.     

Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions

Closely related to studying the function of a protein is the analysis of its three-dimensional structure and the identification of interaction sites with its binding partners. An alternative approach to the high-resolution methods for three-dimensional protein structure analysis, such as X-ray crystallography and NMR spectroscopy, consists of covalently connecting two functional groups of the protein(s) under investigation. The location of the created cross-links imposes a distance constraint on the location of the respective side chains and allows one to draw conclusions on the three-dimensional structure of the protein or a protein complex. Recently, chemical cross-linking of proteins has been combined with a mass spectrometric analysis of the created cross-linked products. This review article describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the different available strategies that employ chemical cross-linking and different mass spectrometric techniques. The challenges for mass spectrometry caused by the enormous complexity of the cross-linking reaction mixtures are emphasized. The various approaches described in the literature to facilitate the mass spectrometric detection of cross-linked products as well as computer software for data analyses are reviewed.