Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses

Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell's lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems.     

质谱在金属抗癌药物与蛋白质相互作用研究中的应用

研究细胞毒性金属抗肿瘤药物与蛋白质的相互作用,以及这种相互作用对药物的细胞摄入、转运、代谢和生物利用度的影响,对金属抗癌药物的结构设计和优化,提高药物的抗癌活性,降低毒副作用具有重要意义。基于软电离技术的电喷雾质谱和基质辅助激光解析电离质谱能够在分析检测过程中很好的保留金属抗癌药物与蛋白质的共价(配位)结合,获得药物与蛋白质结合位点的信息。同时,质谱分析还具有灵敏度高,所需样品量少,耗时短以及适用于分析复杂生物样品等优点,已成为研究金属抗癌药物与蛋白质相互作用最强有力的工具,在为药物发现提供大量化学、生物信息的同时,也极大地促进了质谱技术自身的发展。本文将结合我们在金属抗癌药物相互作用组学研究中取得的最新进展,系统地总结、评述Bottom-up和Top-down质谱分析方法在铂、钌类金属抗癌药物与蛋白质相互作用研究中的发展动态,并分析这一前沿交叉领域未来的发展趋势。     

Analytical strategies for identifying drug metabolites

With the dramatic increase in the number of new chemical entities (NCEs) arising from combinatorial chemistry and modern high-throughput bioassays, novel bioanalytical techniques are required for the rapid determination of the metabolic stability and metabolites of these NCEs. Knowledge of the metabolic site(s) of the NCEs in early drug discovery is essential for selecting compounds with favorable pharmacokinetic credentials and aiding medicinal chemists in modifying metabolic "soft spots". In development, elucidation of biotransformation pathways of a drug candidate by identifying its circulatory and excretory metabolites is vitally important to understand its physiological effects. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have played an invaluable role in the structural characterization and quantification of drug metabolites. Indeed, liquid chromatography (LC) coupled with atmospheric pressure ionization (API) MS has now become the most powerful tool for the rapid detection, structure elucidation, and quantification of drug-derived material within various biological fluids. Often, however, MS alone is insufficient to identify the exact position of oxidation, to differentiate isomers, or to provide the precise structure of unusual and/or unstable metabolites. In addition, an excess of endogenous material in biological samples often suppress the ionization of drug-related material complicating metabolite identification by MS. In these cases, multiple analytical and wet chemistry techniques, such as LC-NMR, enzymatic hydrolysis, chemical derivatization, and hydrogen/deuterium-exchange (H/D-exchange) combined with MS are used to characterize the novel and isomeric metabolites of drug candidates. This review describes sample preparation and introduction strategies to minimize ion suppression by biological matrices for metabolite identification studies, the application of various LC-tandem MS (LC-MS/MS) techniques for the rapid quantification and identification of drug metabolites, and future trends in this field.     

Localizing and extracting filament distributions from microscopy images

Detailed quantitative measurements of biological filament networks represent a crucial step in understanding architecture and structure of cells and tissues, which in turn explain important biological events such as wound healing and cancer metastases. Microscopic images of biological specimens marked for different structural proteins constitute an important source for observing and measuring meaningful parameters of biological networks. Unfortunately, current efforts at quantitative estimation of architecture and orientation of biological filament networks from microscopy images are predominantly limited to visual estimation and indirect experimental inference. Here, we describe a new method for localizing and extracting filament distributions from 2D microscopy images of different modalities. The method combines a filter‐based detection of pixels likely to contain a filament with a constrained reverse diffusion‐based approach for localizing the filaments centrelines. We show with qualitative and quantitative experiments, using both simulated and real data, that the new method can provide more accurate centreline estimates of filament in comparison to other approaches currently available. In addition, we show the algorithm is more robust with respect to variations in the initial filter‐based filament detection step often used. We demonstrate the application of the method in extracting quantitative parameters from confocal microscopy images of actin filaments and atomic force microscopy images of DNA fragments.     

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     

液相色谱-串联质谱生物分析方法的基质效应和对策

液相色谱-串联质谱（LC-MS/MS）法具有高灵敏度、高选择性、高通量等特点,已经成为生物分析的主流方法,广泛应用于新药发现和开发过程中新化学实体及其代谢物的定量分析。然而,由于生物样品基质成分复杂,共洗脱物质会影响分析物的离子化,使分析物的质谱响应增加或降低,从而影响LC-MS/MS分析方法的准确度和精密度。一般而言,离子抑制较离子增强更为常见。因此,在建立LC-MS/MS法时,需要对离子抑制进行评估和校正,并采用不同的策略消除或减少基质效应的影响。本文综述了生物样品分析中基质效应的来源和评估方法,重点介绍了克服基质效应的策略。引起基质效应的物质包括磷脂、盐类、尿素、代谢物等内源性物质和赋形剂、抗凝剂、固定相释放物质及降解产物等外源性物质。目前基质效应的评价方法主要有提取后加入法和柱后灌注法。克服基质效应的策略主要有使用稳定同位素内标,将极性药物衍生化,沉淀蛋白后稀释上清液,优化样品预处理方法、色谱和质谱条件等。结合本课题组的应用实例,重点阐述了建立LC-MS/MS生物分析方法时,为减少基质效应遇到的困难及解决方法。     

基于加工特征的复合快速成形技术研究

结合分层制造和数控加工的技术优势,提出了一种以六轴并联机床为切削加工平台、基于加工特征的复合快速成形方法。利用Parasolid modeling kernel开发了具有加工特征提取与消除、分层处理等功能的数据处理软件系统。以顶针座零件为对象进行了原型制作实验,整个制作过程需要8h,制作精度为0.05mm,与SLA方法相比具有较高的成形效率和精度。     

Experimental investigation of new manufacturing process chains to create micro-metal structures on polymer substrates for lab-on-chip sensors

Over the last two decades, lab-on-a-chip devices have emerged as a leading technology for life sciences, drug development, medical diagnostics, food safety, agricultural and environmental monitoring. The conventional methods used nowadays to manufacture these micro- and nano-functional surface topography are very expensive, and they do not fit the requirements for industrial production. In particular, we report an experimental investigation to link technologies as structuring process and replication processes by establishing through the proposed low-cost-based approaches new manufacturing process chains to process non-silicon materials devices, which integrate sub-μ periodic structures. Moreover, we introduce a prototype of new testing equipment working in a non-clean environment based on photolithographic procedures. μ-trenches with feature size in the order of 10?μm are integrated on cyclic olefin co-polymer substrates. The achievements authorize to consider the proposed process chain a valid option to fabricate structured surface topography in the sub-μ range for biological applications.     

Mass spectrometry for the quantification of bioactive peptides in biological fluids

The study of pharmacologically active peptides is central to the understanding of disease and development of novel therapies. It would be advantageous to monitor the fate of bioactive peptides in biological fluids and tissues following their in vivo administration (exogenous administration) or the modulation of endogenous factors (e.g., peptide hormones) affected by the administration of a pharmacological agent. Measurement of administered compounds (small molecules) in plasma is a mature field. However, measurement of pharmacologically active peptides presents particular problems for quantitative mass spectrometry, including challenges from selectivity and sensitivity perspectives. Current approaches towards peptide quantification in biological fluids include immunoassays and mass spectrometric techniques. Immunoassays, although sensitive, lack the necessary selectivity for distinction between peptide and metabolites. Modified molecules induced by metabolic transformations (e.g., N- or C-terminal truncation of the peptide) might not be differentiated by the antibody used in the assay, leading to cross-reactivity. However, although it is generally accepted that mass spectrometry is an ideal technique for the quantification of trace levels of analytes in biological fluids, immunological techniques are still characterized by better limits of peptide detection. In this review article, novel mass spectrometric approaches and strategies on peptide quantification will be described. The current capabilities and prospects for advances in this critical area of research will be examined.     

Retracted: Localizing and extracting filament distributions from microscopy images

Detailed quantitative measurements of biological filament networks represent a crucial step in understanding architecture and structure of cells and tissues, which in turn explain important biological events such as wound healing and cancer metastases. Confocal microscope images of biological specimens marked for different structural proteins constitute an important source for observing and measuring meaningful parameters of biological networks. Unfortunately, current efforts at quantitative estimation of architecture and orientation of biological filament networks from microscopy images are predominantly limited to visual estimation and indirect experimental inference. Here we describe a new method for localizing and extracting filament distributions from 2D confocal microscopy images. The method combines a filter‐based detection of pixels likely to contain a filament with a constrained reverse diffusion‐based approach for localizing the filaments centrelines. We show with qualitative and quantitative experiments, using both simulated and real data, that the new method can provide more accurate centreline estimates of filament in comparison to other approaches currently available. In addition, we show the algorithm is more robust with respect to variations in the initial filter‐based filament detection step often used. We demonstrate the application of the method in extracting quantitative parameters from an experiment that seeks to quantify the effects of carbon nanotubes on actin cytoskeleton in live HeLa cells. We show that their presence can disrupt the overall actin cytoskeletal organization in such cells.     

Surgical robotics: A look-back of latest advancement and bio-inspired ways to tackle existing challenges

This article is dedicated to present a review on existing challenges and latest developments in surgical robotics in attempts to overcome the obstacles lying behind. Rather than to perform an exhaustive evaluation, we would emphasize more on the new insight by digesting the emerging bio-inspired surgical technologies with potentials to revolutionize the field. Typical approaches, possible applications, advantages and technical challenges were discussed. Evolutions of surgical robotics and future trends were analyzed. It can be found that, the major difficulties in the field of surgical robots may not be properly addressed by only using conventional approaches. As an alternative, bio-inspired methods or materials may shed light on new innovations. While endeavors to deal with existing strategies still need to be made, attentions should be paid to also borrow ideas from nature.     

基于高分辨质谱技术的整体动物体内药物成像分析新方法研究

质谱分子成像技术作为体内药物分析的新兴工具受到越来越多的关注,其中生物体内复杂基质的干扰是面临的关键问题之一。本研究利用高分辨质谱技术的优势,采用空气动力辅助离子化质谱成像方法（AFAI-MSI）,建立了高特异性的整体动物体内药物成像分析新方法,以提高体内药物成像分析结果的准确性和可靠性。以候选新药右旋娃儿藤宁碱（S-(+)-deoxytylophorinidine, CAT）为研究对象,采用高分辨质谱全扫描与靶向扫描相结合的方式,对整体动物体内药物的分布进行AFAI-MSI分析。结果表明,该方法能够准确地反映药物特异性分布和处置情况。通过一次质谱成像实验,从整体动物水平同时实现了候选新药体内分布和药物干预下内源性代谢物的成像分析,为候选新药的早期研发提供思路与手段。     

Current engineering and clinical aspects of needle-free injectors: A review

Needle-free injectors can be used to achieve non-invasive drug delivery by impregnating biological barriers. They are considered as the future of drug delivery and therapeutic applications. The history of needle-free injectors dates back to the 1940s and these devices have been constantly evolving since then. Their operating principles and applications have been improved over the years. Herein, we review the current engineering mechanisms and clinical aspects of needle-free microjet injectors. The present study focuses on using engineering approaches to deal with various factors that affect the penetration and dispersion characteristics of the microjet.     

液相色谱-质谱联用技术在药物代谢产物鉴定中的应用

药物代谢研究贯穿药物开发的整个过程。生物基质中药物代谢产物的快速、准确鉴定有助于理解药物或候选化合物的生物转化途径,确定代谢软位点,从而帮助优化先导物结构,筛选出具有更高代谢稳定性的药物。利用亲核性捕获试剂开展体外代谢实验,检测反应性代谢产物的生成,相关结果可以帮助规避候选化合物进入临床后可能产生的毒性风险。由于液相色谱-质谱联用技术（LC/MS）具有分析通量高、检测灵敏度高、选择性好、能提供丰富的结构相关信息等优点,其在药物代谢研究中的作用越来越重要。本工作综述了近年来作者所在实验室采用LC/MS法开展的药物代谢产物鉴定研究,提出了基于LC/MS技术的药物代谢产物鉴定研究的基本流程和药物在人体内的主要代谢产物,可为临床药动学研究和药物相互作用研究提供数据基础。     

Peptide and protein drugs: the study of their metabolism and catabolism by mass spectrometry

Peptide and protein drugs have evolved in recent years into mainstream therapeutics, representing a significant portion of the pharmaceutical market. Peptides and proteins exhibit highly diverse structures, broad biological activities as hormones, neurotransmitters, structural proteins, metabolic modulators and therefore have a significant role as both therapeutics and biomarkers. Understanding the metabolism of synthetic or biotechnologically derived peptide and protein drugs is critical for pharmaceutical development as metabolism has a significant impact on drug efficacy and safety. Although the same principles of pharmacokinetics and metabolism of small molecule drugs apply to peptide and protein drugs, there are few notable differences. Moreover, the study of peptide and protein drug metabolism is a rather complicated process which requires sophisticated analytical techniques, and mass spectrometry based approaches have provided the capabilities for efficient and reliable quantification, characterization, and metabolite identification. This review article will focus on the current use of mass spectrometry for the study of the metabolism of peptide and protein drugs.     

我国节能与新能源汽车发展战略与对策

随着我国经济的快速发展,国家越来越重视节能与新能源汽车的发展战略.为了进一步的提升节能与新能源汽车发展质量,要根据实际情况开发多种新能源产品,因此本文主要针对我国节能与新能源汽车发展战略与对策进行简要分析,并提出合理化建议.     

New separation tools for comprehensive studies of protein expression by mass spectrometry

Mass spectrometry has emerged as a core technique for protein identification and characterization because of its high sensitivity, accuracy, and speed of analysis. The most widespread strategy for studying global protein expression in biological systems employs analytical two-dimensional polyacrylamide gel electrophoresis (2D PAGE) followed by enzymatic degradation of isolated protein spots, peptide mapping, and bioinformatics searches. Using this method, thousands of proteins can be resolved in a gel and their expression quantified. However, certain types of proteins possessing important cellular functions are not easily analyzed using this strategy. These proteins include membrane, low copy number, highly basic, and very large (> 150 kDa) and small (< 10 kDa) proteins. To meet the growing need to simultaneously monitor all types of proteins in a biological system, new separation strategies have emerged that are amenable to hyphenation to mass spectrometric techniques. This article will review these new techniques and examine their usefulness in studies of protein expression.     

In vitro models for bone mechanobiology: applications in bone regeneration and tissue engineering

Healthy bone healing is a remarkable, mechanically sensitive, scar-free process that leads rapidly to repair tissue of high mechanical quality and functionality, and knowledge of this process is essential for driving advances in bone tissue engineering and regeneration. Gaining this knowledge requires the use of models to probe and understand the detailed mechanisms of healing, and the tight coupling of biology and mechanics make it essential that both of these aspects are controlled and analysed together, using a mechanobiological approach. This article reviews the literature on in vitro models used for this purpose, beginning with two-dimensional (2D) cell culture models used for applying controlled mechanical stimuli to relevant cells, and detailing the analysis techniques required for understanding both substrate strain and fluid flow stimuli in sufficient detail to relate them to biological response. The additional complexity of three-dimensional (3D) models, enabling more faithful representation of the healing situation, can require correspondingly more sophisticated tools for mechanical and biological analysis, but has recently uncovered exciting evidence for the mechanical sensitivity of angiogenesis, essential for successful healing. Studies using explanted tissue continue to be vital in informing these approaches, providing additional evidence for the relevance of effects in biological and mechanical environments close to those in the living organism. Mechanobiology is essential for the proper analysis of models for bone regeneration, and has an exciting integrative role to play not only in advancing knowledge in this area, but also in ensuring successful translation of new tissue engineering and regenerative therapies to the clinic.     

Inhibition of angiogenesis at endothelial cell level

Targeting of proliferating endothelial cells may allow a new therapeutic strategy against malignant tumors. Endothelial cells are easily accessible through the blood stream and genetically stable, reducing the possibility of acquiring drug resistance. There are numerous candidates for angiogenesis targets of drug development, e.g. a single endothelial cell has 2,000-20,000 different receptors on a cell membrane and inside a cell there are hundreds of second messengers. Inhibitors that are active at endothelial cells can be placed in three main groups inducing blockage of endothelial cell activator, direct inhibition of endothelial cells, inhibition of endothelial specific signaling. This review summarizes different approaches already in clinical trials. Specific effort is taken to give a view of and a new perspective over clinically relevant basic mechanisms, e.g. VEGF, ETS and radionanotargeting. It is clear that aggressive development work both at the preclinical and clinical levels is still needed; however, breakthroughs in applied therapies are expected at any time.     

高效液相色谱-高分辨质谱法研究药物代谢产物的数据处理策略

高效液相色谱-高分辨质谱（HPLC-HRMS）联用技术具有高灵敏度、快速和高质量准确度的特点,是药物代谢产物分析的有力手段。通过使用HPLC-HRMS产生高分辨质谱数据（高分辨质量数、多级质谱数据、同位素分布）,结合多重采集后数据处理技术,可用于药物代谢产物的快速发现和结构鉴定。本工作综述了近年来基于HPLC-HRMS技术应用最为广泛的几种数据挖掘策略及应用,如,提取离子色谱、质量亏损过滤、同位素过滤、本底扣除、产物离子过滤、质谱树状图过滤、SWATH和MS^E以及这些技术的联用等。通过合理地使用其中一种或几种策略对HPLC-HRMS产生的数据进行处理,可以有效地进行药物代谢产物的发现和鉴定。