高速多通道遥感相机快视系统的实现

针对目前遥感相机输出通道多、数据率高和像素灰阶高等特点,提出并构建了基于现场可编程门阵列(FPGA)并行处理技术的快视系统。该系统主要由存储单元、预处理单元以及高清显示单元等核心部件组成。存储单元采用FPGA直接控制大容量SATA磁盘阵列实现高速海量存储;预处理单元实时对高速海量图像数据进行缩放、平移和数据融合等操作,克服传统快视系统无法高速处理海量图像数据的技术瓶颈;高清显示单元驱动3台12位显示器进行高灰阶、大幅面无缝拼接显示,弥补以往对高灰阶遥感图像只能截断显示的缺陷。实验结果表明：该系统存储容量达96 TB,可对总速率高达19.7 Gb/s 的12通道12位量化遥感图像数据进行实时记录与无失真显示。系统工作稳定可靠,易于扩展,已成功运用于遥感相机的研制测试中,大大提高了遥感相机的研制效率。     

Tools and strategies for visualization of large image data sets in high-resolution imaging mass spectrometry

Mass spectrometry based proteomics is one of the scientific domains in which experiments produce a large amount of data that need special environments to interpret the results. Without the use of suitable tools and strategies, the transformation of the large data sets into information is not easily achievable. Therefore, in the context of the virtual laboratory of enhanced science, software tools are developed to handle mass spectrometry data sets. Using different data processing strategies for visualization, it enables fast mass spectrometric imaging of large surfaces at high-spatial resolution and thus aids in the understanding of various diseases and disorders. This article describes how to optimize the handling and processing of the data sets, including the selection of the most optimal data formats and the use of parallel processing. It also describes the tools and solutions and their application in mass spectrometric imaging strategies, including new measurement principles, image enhancement, and image artifact suppression.     

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     

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.     

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.     

Informatics development: challenges and solutions for MALDI mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been successfully applied to elucidating biological questions trough the analysis of proteins, peptides, and nucleic acids. Here, we review the different approaches for analyzing the data that is generated by MALDI-MS. The first step in the analysis is the processing of the raw data to find peaks that correspond to the analytes. The peaks are characterized by their areas (or heights) and their centroids. The peak area can be used as a measure of the quantity of the analyte, and the centroid can be used to determine the mass of the analyte. The masses are then compared to models of the analyte, and these models are ranked according to how well they fit the data and their significance is calculated. This allows the determination of the identity (sequence and modifications) of the analytes. We show how this general data analysis workflow is applied to protein and nucleic acid chemistry as well as proteomics.     

非定向筛查数据非依赖采集策略研究进展

数据采集方式是质谱分析的关键步骤,是影响实验效率以及结果准确度的重要因素。较之于传统的数据采集方式,近年来出现的数据非依赖采集技术具有高通量、高覆盖度、高准确性等优势,从而成为蛋白组学与代谢产物定量和组学研究的强有力工具,对食品分析领域有重要的参考和借鉴价值。综述了目前主要的几种数据非依赖采集原理和数据处理最新进展并突出了在食品分析中的非定向筛查潜力,总结了非定向筛查数据非依赖采集在食品安全性分析、食品真实性分析,食品中功能活性成分分析的应用。最后探讨数据非依赖采集在食品分析中面临的挑战和未来发展趋势。     

MALDI-TOF mass spectrometry of bacteria

The development of MALDI-TOF mass spectrometry methods for the characterization of bacteria is reviewed and discussed. The general use of MALDI for the characterization of large biomolecules led directly to obvious applications involving the analysis of isolated bacterial proteins. More surprising was the observation that MALDI-TOF mass spectrometry could be applied directly to crude cellular fractions or cellular suspensions and that the resulting data from such complex mixtures could provide evidence for chemotaxonomic classification. Versatility and the rapidity of analysis led to the rapid development of a number of MALDI-TOF methods involving bacteria. Examples of some of the applications covered in this review are the analysis of bacterial RNA and DNA, the detection of recombinant proteins, the characterization of targeted or unknown proteins, bacterial proteomics, the detection of virulence markers, and the very rapid characterization of bacteria at the genus, species, and strain level. The demonstrated capability of taxonomic classification at the strain level, using unprocessed cells, opens the possibility that MALDI-TOF and similar mass spectrometry approaches may contribute significantly to fulfilling emerging needs for the development of near real-time methods for the characterization of bacteria.     

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     

面向大规模定制设计的并行设计方法研究及应用

针对大规模定制设计的特点,提出了基于参数化CAD和PDM系统的并行设计平台框架,探讨了基于该平台进行产品变型式并行设计的流程和方法。应用表明,该方法可较好地解决变型产品设计过程中的产品数据重用问题。     

Phosphoproteomics by mass spectrometry and classical protein chemistry approaches

The general fields of biological sciences have seen phenomenal transformations in the past two decades at the level of data acquisition, understanding biological processes, and technological developments. Those advances have been made partly because of the advent of molecular biology techniques (which led to genomics) coupled to the advances made in mass spectrometry (MS) to provide the current capabilities and developments in proteomics. However, our current knowledge that approximately 30,000 human genes may code for up to 1 million or more proteins disengage the interface between the genome sequence database algorithms and MS to generate a major interest in independent de novo MS/MS sequence determination. Significant progress has been made in this area through procedures to covalently modify peptide N- and C-terminal amino-acids by sulfonation and guanidination to permit rapid de novo sequence determination by MS/MS analysis. A number of strategies that have been developed to perform qualitative and quantitative proteomics range from 2D-gel electrophoresis, affinity tag reagents, and stable-isotope labeling. Those procedures, combined with MS/MS peptide sequence analysis at the subpicomole level, permit the rapid and effective identification and quantification of a large number of proteins within a given biological sample. The identification of proteins per se, however, is not always sufficient to interpret biological function because many of the naturally occurring proteins are post-translationally modified. One such modification is protein phosphorylation, which regulates a large array of cellular biochemical pathways of the biological system. Traditionally, the study of phosphoprotein structure-function relationships involved classical protein chemistry approaches that required protein purification, peptide mapping, and the identification of the phosphorylated peptide regions and sites by N-terminal sequence analysis. Recent advances made in mass spectrometry have clearly revolutionized the studies of phosphoprotein biochemistry, and include the development of specific strategies to preferentially enrich phosphoproteins by covalent-modifications that incorporate affinity tags that use the physicochemical properties of phosphoaminoacids. The phosphoserine/phosphothreonine-containing proteins/peptides are derivatized under base-catalyzed conditions by thiol agents; mono- and di-thiol reagents both have been used in such studies. The thiol agent may have: (i) an affinity tag for protein enrichment; (ii) stable-isotopic variants for relative quantitation; or (iii) a combination of the moieties in (i) and (ii). These strategies and techniques, together with others, are reviewed, including their practical application to the study of phosphoprotein biochemistry and structure-function. The consensus of how classical protein chemistry and current MS technology overlap into special case of proteomics, namely "phosphoproteomics," will be discussed.     

40MHz高速采集与通信模块在超声检测中的应用

设计了以AD9057为核心的采样频率为40 MHz的高速采集和通信模块。选用具有USB通信功能的C8051F340单片机,通过分时存取的方法进行超声波信号的采集和大量数据的传输,并通过上位机进行波形显示和数据处理。实验证明,40 MHz高速采集与通信模块在超声波探伤系统中应用稳定、准确、可靠。     

Analyzing the evolution of the opioid/orphanin gene family

Advances in molecular biology have made it possible to rapidly obtain the amino acid sequence of neuropeptide precursors-either by cloning and sequencing the cDNA that encodes the precursor, or by reconstructing the arrangement of exons and introns in a neuropeptide-coding gene through genomic approaches. The databases generated from these molecular approaches have been used to design probes to identify the cells that express the gene, or to ascertain the rate of expression of the gene, and even to predict the post-translational modifications that can generate functional neuropeptides from a biologically inert precursor. Although the power of these approaches is substantial, it is appreciated that a gene sequence or an mRNA sequence reflects the potential products that may be assembled in a secretory cell. To understand the functional capabilities of the secretory cell, the molecular genetics approaches must be combined with procedures that actually characterize the end-products generated by the secretory cell. Recent advances in two-dimensional gel electrophoresis and mass spectrometry now make it possible to analyze neuropeptides from a relatively small amount of tissue. These procedures can reveal novel end-products, tissue-specific endoproteolytic cleavage events, and developmental shifts in post-translational processing schemes. A gene family that illustrates all of these processes and the advantages of combining genomics with proteomics is the opioid/orphanin gene family.     

小型化弹丸速度测试系统

提出了一种基于光幕测速和单片机数据处理的小型化的弹丸速度测试系统。采用半导体激光器、光电探测器、原向反射屏形成大面积光幕测试区,当弹丸穿越光幕时,光通量的变化被光电探测器转变为电信号,经过比较电路后送入单片机进行数据处理,并由LED进行速度显示。文中对测试原理和测试系统的光学设计单元、信号处理单元及数据采集、显示单元进行了介绍,并对该系统进行了壬7．62mm弹丸速度测试,给出了测试数据。试验表明,该测速系统具有灵敏度高、体积小、成本低、使用方便、灵活、工作可靠等优点。     

Liquid chromatography combined with mass spectrometry for 13C isotopic analysis in life science research

Among the different disciplines covered by mass spectrometry, measurement of (13)C/(12)C isotopic ratio crosses a large section of disciplines from a tool revealing the origin of compounds to more recent approaches such as metabolomics and proteomics. Isotope ratio mass spectrometry (IRMS) and molecular mass spectrometry (MS) are the two most mature techniques for (13)C isotopic analysis of compounds, respectively, for high and low-isotopic precision. For the sample introduction, the coupling of gas chromatography (GC) to either IRMS or MS is state of the art technique for targeted isotopic analysis of volatile analytes. However, liquid chromatography (LC) also needs to be considered as a tool for the sample introduction into IRMS or MS for (13)C isotopic analyses of non-volatile analytes at natural abundance as well as for (13)C-labeled compounds. This review presents the past and the current processes used to perform (13)C isotopic analysis in combination with LC. It gives particular attention to the combination of LC with IRMS which started in the 1990's with the moving wire transport, then subsequently moved to the chemical reaction interface (CRI) and was made commercially available in 2004 with the wet chemical oxidation interface (LC-IRMS). The LC-IRMS method development is also discussed in this review, including the possible approaches for increasing selectivity and efficiency, for example, using a 100% aqueous mobile phase for the LC separation. In addition, applications for measuring (13)C isotopic enrichments using atmospheric pressure LC-MS instruments with a quadrupole, a time-of-flight, and an ion trap analyzer are also discussed as well as a LC-ICPMS using a prototype instrument with two quadrupoles.     

Automated protein identification by tandem mass spectrometry: issues and strategies

Protein identification by tandem mass spectrometry (MS/MS) is key to most proteomics projects and has been widely explored in bioinformatics research. Obtaining good and trustful identification results has important implications for biological and clinical work. Although well matured, automated software identification of proteins from MS/MS data still faces a number of obstacles due to the complexity of the proteome or procedural issues of mass spectrometry data acquisition. Expected or unexpected modifications of the peptide sequences, polymorphisms, errors in databases, missed or non-specific cleavages, unusual fragmentation patterns, and single MS/MS spectra of multiple peptides of the same m/z are so many pitfalls for identification algorithms. A lot of research work has been carried out in recent years that yielded new strategies to handle a number of these issues. Multiple MS/MS identification algorithms are now available or have been theoretically described. The difficulty resides in choosing the most adapted method for each type of spectra being identified. This review presents an overview of the state-of-the-art bioinformatics approaches to the identification of proteins by MS/MS to help the reader doing the spade work of finding the right tools among the many possibilities offered.     

Lab-on-a-ChipforProteomics

Proteomics is a major component of systems biology. Mass spectrometry is an enabling technology for proteomics. To fully realize the enormous potential of lab-on-a-chip in proteomics, major advance in interfacing microfluidics with mass spectrometry is needed. We have demonstrated the monolithic integration of a microfluidic channel with multinozzle electrospray emitters via a novel silicon microfabrication process. These microfabricated monolithic multinozzle emitters (M3 emitters) can be readily mass-produced from silicon wafers. Each emitter consists of a parallel silica nozzle array protruding out from a hollow silicon sliver stem with the conduit size of 100×10 micron. The dimension and number of freestanding nozzles can be systematically and precisely controlled during the fabrication process. The M3 emitters showed comparable performance to that of the commercial tips in terms of stability and sensitivity for standard peptides and high molecular weight proteins. Multinozzle emitters are expected to ease back pressure and clogging problem that single nozzle emitters have to cope with, especially as the channel downsizes to submicron scale. Our current work aims to further integrate M3 emitters with the front-end sample processing on a chip. New developments in optimizing the performance of M3 emitters for potential applications in single cell analysis will be discussed.     

一种基于iSRM策略的蛋白质组质谱数据分析工具

由于重复性好、定量精度高,基于质谱的选择反应监测（SRM）技术在蛋白质定量分析中的应用越来越广泛。智能选择反应监测（iSRM）是一种新型的SRM实验策略。针对该策略产生的质谱数据,开发了一个肽段定量信息提取工具--iSQuant。该工具使用MATLAB脚本语言编写,简便易用。利用重复实验数据和标准实验数据对iSQuant的性能评估表明,iSQuant具有优越的可重复性能,定量结果和理论丰度线性度很高。     

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...     

显示信息高速串行传输的差错控制

提出了差错控制编码方法来解决LED大屏幕远程通信系统显示信息高速率串行传输数据可靠性降低的问题.考虑到显示信息发送端和接收端的硬件基础及实现要求不同,提出在发送端采用并行算法结构,并构造了生成矩阵进行编码运算来提高算法的实时性;在接收端采用双时钟串行循环译码电路结构,在伴随式计算后采用高速时钟进行纠错,使得码字较长的编码仍旧能够获得较低的硬件开销并具备较好的实时译码能力.实验及理论分析表明,提出的方案能够实现高效率的编解码运算,编码效率达到98.2％.该方案也有效地降低了误码率,实际应用中误码率至少降低了1个数量级.使用提出的方案实现了显示信息的高速率、高效率串行传输.