Plant proteomics: concepts, applications, and novel strategies for data interpretation

Proteomics is an essential source of information about biological systems because it generates knowledge about the concentrations, interactions, functions, and catalytic activities of proteins, which are the major structural and functional determinants of cells. In the last few years significant technology development has taken place both at the level of data analysis software and mass spectrometry hardware. Conceptual progress in proteomics has made possible the analysis of entire proteomes at previously unprecedented density and accuracy. New concepts have emerged that comprise quantitative analyses of full proteomes, database-independent protein identification strategies, targeted quantitative proteomics approaches with proteotypic peptides and the systematic analysis of an increasing number of posttranslational modifications at high temporal and spatial resolution. Although plant proteomics is making progress, there are still several analytical challenges that await experimental and conceptual solutions. With this review I will highlight the current status of plant proteomics and put it into the context of the aforementioned conceptual progress in the field, illustrate some of the plant-specific challenges and present my view on the great opportunities for plant systems biology offered by proteomics.     

眼倍率色差的实验测定与理论分析

提供一种计算人眼倍率色差的简化模型。理论分析得：倍率色差与轴向色差，以及人射光瞳至节．点问轴向距离成正比。眼睛观察前五平行平面视觉倾斜对视网膜成像大小非常敏感，利用这种技术，通过一个辅助连镜可以测量人眼双眼倍率色差的平均值，从而得到单眼的倍丰色差．对实验结果作分析，可得与理论模型相一致的关系。     

新冠病毒蛋白及其细胞受体ACE2翻译后修饰的质谱分析

新冠肺炎(COVID-19)在全世界范围内造成了巨大的健康危机和不可估量的损失.新出现的变种病毒株表明,新冠病毒(SARS-CoV-2)可能会像流感病毒一样在人类社会中继续流行,成为一种长久的健康威胁.控制新冠病毒的传染和开发有效的治疗方法迫在眉睫.因此,找到合适的生物标志物以表明病理和生理状态是当务之急.蛋白质是生命...     

Proteome analysis in the study of lymphoma cells

This review provides an overview on recent studies in the field of proteome analysis of lymphoma cells, and highlights the potentials of such studies for a better knowledge of drug effects at the molecular level. After giving general information on the field of proteome analysis of lymphoma cells, some characteristics of the strategies used during this analysis are pointed out, such as cell extraction strategies and affinity captures. Therefore, the issue of proteome analysis of lymphoma cells content will be covered with respect to those protein extracts that can be prepared in saline solutions, such as cytoplasm proteins, or that are associated with the cell membranes. The question of which kinds of information have been retrieved from lymphoma-cell proteomics is discussed on the basis of several examples-lymphoma cell-mapping studies and constitution of protein databases, and comparative proteome analysis studies of the modifications that result from a drug treatment.     

Proteomics by FTICR mass spectrometry: top down and bottom up

This review provides a broad overview of recent Fourier transform ion cyclotron resonance (FTICR) applications and technological developments relevant to the field of proteomics. Both the "bottom up" (peptide level) and "top down" (intact protein level) approaches are discussed and illustrated with examples. "Bottom up" topics include peptide fragmentation, the accurate mass and time (AMT) tag approach and dynamic range extension technology, aspects of quantitative proteomics measurements, post-translational modifications, and developments in FTICR operation software focused on peptide and protein identification. Topics related to the "top down" approach include various aspects of high mass measurements, protein tandem mass spectrometry, methods for the study of protein conformations, and protein complexes as well as advanced technologies that may become of practical utility in the coming years. Finally, early examples of the integration of both FTICR approaches to biomedical proteomics applications are presented, along with an outlook for future directions.     

Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research

Progress in proteomics research has led to a demand for powerful analytical tools with high separation efficiency and sensitivity for confident identification and quantification of proteins, posttranslational modifications, and protein complexes expressed in cells and tissues. This demand has significantly increased interest in capillary electrophoresis‐mass spectrometry (CE‐MS) in the past few years. This review provides highlights of recent advances in CE‐MS for proteomics research, including a short introduction to top‐down mass spectrometry and native mass spectrometry (native MS), as well as a detailed overview of CE methods. Both the potential and limitations of these methods for the analysis of proteins and peptides in synthetic and biological samples and the challenges of CE methods are discussed, along with perspectives about the future direction of CE‐MS. @ 2019 Wiley Periodicals, Inc. Mass Spec Rev 00:1–16, 2019.     

Discovery of Novel Biochemical Pathways Using Proteomics Approaches

Extensive studies in histones and p53 suggest that these proteins can be modified by an array of protein post-translational modifications (PTMs), most of which are correlated with important biological functions. Nevertheless, PTM types and their sites in other proteins remain largely unknown, except several widely studied ones. The information deficiency suggests an urgent need for reliable technology for characterization of all the PTMs in a protein and for their dynamic studies. To this end, we recently developed an unrestrictive protein sequence alignment algorithm, PTMap, and used it in conjunction with mass spectrometry for accurate identification of all the possible PTMs, known or undescribed ones. We have used the algorithm to identify novel PTMs, to discover common in vitro protein modifications, to study PTM cross-talks, and to study protein mutations. In this presentation, applications of such mass spectrometry-based proteomics technologies will be discussed.     

基于质谱的蛋白质组学方法新进展

蛋白质组学是后基因组时代的科研热点,其研究方向主要涵盖蛋白质表达谱、蛋白质翻译后修饰谱、蛋白质相互作用谱和单细胞蛋白质组等定性分析以及相对和绝对定量分析,现已广泛应用于生物、医药及病理研究中.由于质谱具有灵敏、准确、高通量等特点,是蛋白质组学研究必不可少的工具.本文综述了近年来基于质谱技术的蛋白质组鉴定及定量方法,并展...     

THE PRESENT AND FUTURE OF THE MASS SPECTROMETRY-BASED INVESTIGATION OF THE EXOSOME LANDSCAPE

Exosomes are critical intercellular messengers released upon the fusion of multivesicular bodies with the cellular plasma membrane that deliver their cargo in the form of extracellular vesicles. Containing numerous nonrandomly packed functional proteins, lipids, and RNAs, exosomes are vital intercellular messengers that contribute to the physiologic processes of the healthy organism. During the post-genome era, exosome-oriented proteomics have garnered great interest. Since its establishment, mass spectrometry (MS) has been indispensable for the field of proteomics research and has advanced rapidly to interrogate biological samples at a higher resolution and sensitivity. Driven by new methodologies and more advanced instrumentation, MS-based approaches have revolutionized our understanding of protein biology. As the access to online proteomics database platforms has blossomed, experimental data processing occurs with more speed and accuracy. Here, we review recent advances in the technological progress of MS-based proteomics and several new detection strategies for MS-based proteomics research. We also summarize the use of integrated online databases for proteomics research in the era of big data. © 2020 John Wiley & Sons Ltd. Mass Spec Rev     

人工晶状体的发展趋势及展望

随着人口老龄化,年龄相关性白内障患者日益增多,通过植入人工晶状体可以使白内障患者的视力基本得到恢复。由于白内障患者对术后的视觉质量要求越来越高,个性化设计的人工晶状体已逐渐在临床上推广使用,而多焦点人工晶状体的出现,则成功解决了单焦点人工晶状体术后难以解决的近视力问题。对人工晶状体的发展历史做了简要的阐述,详细地说明了单焦点和多焦点人工晶状体的设计思想及特点,介绍了多焦点人工晶状体的发展现状,最后对人工晶状体未来的发展进行了展望。     

Peptide mapping of proteins in human body fluids using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Human body fluids have been rediscovered in the post-genomic era as great sources of biological markers and perhaps particularly as sources of potential protein biomarkers of disease. Analytical tools that allow rapid screening, low sample consumption, and accurate protein identification are of great importance in studies of complex biological samples and clinical diagnosis. Mass spectrometry is today one of the most important analytical tools with applications in a wide variety of fields. One of the fastest growing applications is in proteomics, or the study of protein expression in an organism. Mass spectrometry has been used to find post-translational modifications and to identify key functions of proteins in the human body. In this study, we review the use of human body fluids as sources for clinical markers and present new data that show the ability of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) to identify and characterize proteins in four human body fluids: plasma, cerebrospinal fluid (CSF), saliva, and urine. The body fluids were tryptically digested without any prior separation, purification, or selection, and the digest was introduced into a 9.4 T FTICR mass spectrometer by direct-infusion electrospray ionization (ESI). Even though these samples represent complex biological mixtures, the described method provides information that is comparable with traditional 2D-PAGE data. The sample consumption is extremely low, a few microliters, and the analysis time is only a few minutes. It is, however, evident that the separation of proteins and/or peptides must be included in the methodology, in order to detect low-abundance proteins and other proteins of biological relevance.     

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     

The scanning near-field optical microscope as a tool for proteomics

The identification of the entire genetic code of human DNA is more or less completed. With this knowledge, research in identifying the real information lying in the genes, will begin. This information is contained in the proteins, which are the main biological actors in the cell. For this reason proteins will be targeted in biological investigations in the future. The structure, affinity and reactivity of each identified protein has to be determined, which is a primary goal in the field of proteomics. This will require new and better strategies to identify protein-protein interaction. Our approach, based on the detection and visualization of single proteins by scanning near-field optical microscopy (SNOM), has allowed us to visualize various fixed and fluorochrome-labelled proteins at the nanometer scale. Subsequently SNOM may then be developed to efficiently detect the specific behavior of a certain protein in response to other biomolecules.     

Cysteine tagging for MS-based proteomics

Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.     

ApplicationofMassSpectrometryinPharmaceuticalDrugDiscoveryResearch

Mass spectrometry has been extensively utilized in drug discovery research and development, from the traditional medicinal chemistry support to drug metabolism and pharmacokinetic studies. As the industry faces with the challenges of tougher diseases and more challenging pathways/targets to tackle, it requires the development of innovative solutions to address needs from target discovery to biomarker identification. It also presents a great opportunity for scientists in the field for innovation, many of which often come from cross disciplinary efforts - chemistry, biology and technology. In this presentation, four areas of drug discovery research where innovative solutions have been developed will be presented: (1) target identification and validation through cellular metabolomic analysis and chemical proteomics; (2) hits discovery and validation using MS-based screening; (3) PK analysis of therapeutic monoclonal antibody; (4) MS imaging for drug tissue distribution. Investment in life saving and life style improving medicines will get more intensified as standard of living improves. Drug discovery research will continue to require and present opportunity for such application driven innovations.     

视线跟踪系统中CCD摄像机的自适应调节

分析了视线跟踪系统中光源、摄像机、眼睛角膜及光斑的几何位置关系,提出了眼睛跟踪策略和一种调光、变焦、聚焦相结合的CCD物镜自动调节方法。对捕获图像进行处理,依据图像灰度均值控制光圈,以适应外部环境光强变化;利用SMD算子大步幅快速粗聚焦,提取图像中光斑信息控制云台瞄准、跟踪眼睛,并进行变焦控制,可在用户头肩图像中自动定位眼睛,适应用户头部位置变化;在眼睛区域自动确定检测窗,在检测窗内使用FSWM聚焦算子判断图像清晰度,实现自动聚焦。若图像中能提取瞳孔信息,则依据瞳孔边缘梯度均值实时调整聚焦。实验表明,在不同外部环境光强及用户在不同使用位置情况下,CCD摄像机通过自适应调节,可实时跟踪眼睛并捕获到清晰眼睛图像。     

Applying proteomics technology to platelet research

Platelets are small enucleated cells that circulate in the blood, where they play a key role in hemostasis and contribute to the formation of vascular plugs. Pathologically, they are involved in thrombosis and heart disease. Because platelets do not have a nucleus, proteomics offers a powerful way to approach their biology. Proteomics technology is based on the huge analytical power offered by mass spectrometry in combination with several separation techniques, such as two-dimensional gel electrophoresis (2DGE) or multidimensional liquid chromatography. Proteomics provides information about the complete set of proteins present in platelets, the platelet proteome, including post-translational variants. Over the last years, several research groups have applied proteomics to platelet research. A detailed analysis of the general proteome and signaling cascades in human platelets will improve our knowledge of platelet function, and thereby aid the development of new therapeutic agents to treat thrombotic diseases. This review presents the major advances in mass spectrometry-based proteomics techniques and their application to platelet research, and analyzes in detail the most relevant contributions to the field.