Collembola, commonly known as springtails, are abundant and important members of soil ecosystems. Due to their small size and hidden life, not much is known about their secondary metabolites. This chemistry is remarkably different from that of insects, with which they share a common ancestor, although they diverged already around 450 mya. Here we describe what is known so far, mainly compounds for chemical defence and cuticular lipids, as well as chemical signals. The uniqueness of the structures found is striking, many of which are not known from other natural sources. These include polychlorinated benzopyranones, small alkaloids, hetero-substituted aromatic compounds, and a diverse terpene chemistry, including highly branched compounds.
{"title":"Small animals with unique chemistry – the natural product chemistry of Collembola","authors":"Anton Möllerke , Stefan Schulz","doi":"10.1039/d4np00049h","DOIUrl":"10.1039/d4np00049h","url":null,"abstract":"<div><div>Covering up to September 2024</div></div><div><div>Collembola, commonly known as springtails, are abundant and important members of soil ecosystems. Due to their small size and hidden life, not much is known about their secondary metabolites. This chemistry is remarkably different from that of insects, with which they share a common ancestor, although they diverged already around 450 mya. Here we describe what is known so far, mainly compounds for chemical defence and cuticular lipids, as well as chemical signals. The uniqueness of the structures found is striking, many of which are not known from other natural sources. These include polychlorinated benzopyranones, small alkaloids, hetero-substituted aromatic compounds, and a diverse terpene chemistry, including highly branched compounds.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 4","pages":"Pages 672-680"},"PeriodicalIF":10.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Arsenic is widely distributed throughout terrestrial and aquatic environments, mainly in highly toxic inorganic forms. To adapt to environmental inorganic arsenic, bacteria have evolved ubiquitous arsenic metabolic strategies by combining arsenite methylation and related redox reactions, which have been extensively studied. Recent reports have shown that some bacteria have specific metabolic pathways associated with structurally and biologically unique organoarsenic natural products. In this highlight, by exemplifying the cases of oxo-arsenosugars, arsinothricin, and bisenarsan, we summarize recent advances in the identification and biosynthesis of bacterial organoarsenic natural products. We also discuss the potential discoveries of novel arsenic-containing natural products of bacterial origins.
{"title":"Recent advances in the biosynthetic studies of bacterial organoarsenic natural products","authors":"Shotaro Hoshino , Hiroyasu Onaka , Ikuro Abe","doi":"10.1039/d4np00036f","DOIUrl":"10.1039/d4np00036f","url":null,"abstract":"<div><div>Covering: 1977 to present</div></div><div><div>Arsenic is widely distributed throughout terrestrial and aquatic environments, mainly in highly toxic inorganic forms. To adapt to environmental inorganic arsenic, bacteria have evolved ubiquitous arsenic metabolic strategies by combining arsenite methylation and related redox reactions, which have been extensively studied. Recent reports have shown that some bacteria have specific metabolic pathways associated with structurally and biologically unique organoarsenic natural products. In this highlight, by exemplifying the cases of oxo-arsenosugars, arsinothricin, and bisenarsan, we summarize recent advances in the identification and biosynthesis of bacterial organoarsenic natural products. We also discuss the potential discoveries of novel arsenic-containing natural products of bacterial origins.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 4","pages":"Pages 663-671"},"PeriodicalIF":10.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as melichuniione A from Melicope chunii.
{"title":"Hot off the Press","authors":"Robert A. Hill , Andrew Sutherland","doi":"10.1039/d5np90011e","DOIUrl":"10.1039/d5np90011e","url":null,"abstract":"<div><div>A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as melichuniione A from <em>Melicope chunii</em>.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 4","pages":"Pages 649-653"},"PeriodicalIF":10.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Total synthesis has been defined as the art and science of making the molecules of living Nature in the laboratory, and by extension, their analogues. At the extremes, specialised metabolites can be created by total chemical synthesis or by total biosynthesis. In this review we explore the advantages and disadvantages of these two approaches using quantitative methodology that combines measures of molecular complexity, molecular weight and fraction of sp3 centres for bioactive fungal metabolites. Total biosynthesis usually involves fewer chemical steps and those steps move more directly to the target than comparable total chemical synthesis. However, total biosynthesis currently lacks the flexibility of chemical synthesis and the ability to easily diversify synthetic routes.
{"title":"Comparing total chemical synthesis and total biosynthesis routes to fungal specialized metabolites","authors":"Dong-Song Tian , Xiao Zhang , Russell J. Cox","doi":"10.1039/d4np00015c","DOIUrl":"10.1039/d4np00015c","url":null,"abstract":"<div><div>Covering the period 1965–2024</div></div><div><div>Total synthesis has been defined as the art and science of making the molecules of living Nature in the laboratory, and by extension, their analogues. At the extremes, specialised metabolites can be created by total chemical synthesis or by total biosynthesis. In this review we explore the advantages and disadvantages of these two approaches using quantitative methodology that combines measures of molecular complexity, molecular weight and fraction of sp<sup>3</sup> centres for bioactive fungal metabolites. Total biosynthesis usually involves fewer chemical steps and those steps move more directly to the target than comparable total chemical synthesis. However, total biosynthesis currently lacks the flexibility of chemical synthesis and the ability to easily diversify synthetic routes.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 4","pages":"Pages 720-738"},"PeriodicalIF":10.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fatty Acyl-AMP Ligases (FAALs) belong to the family of adenylate-forming enzymes and activate fatty acyl substrates through adenylation. FAALs were discovered as key players in various natural product biosynthetic pathways, particularly in the assembly of polyketides and non-ribosomal peptides. These enzymes exhibit a conserved structural architecture that distinguishes them from their close relatives, the Fatty Acyl-CoA Ligases. FAALs display the starter unit in the biosynthesis of diverse natural products where they shuttle fatty acyl substrates into secondary metabolism for further chain elongation and/or modification. In this review, we cover the discovery, distribution and structure of FAALs as well as their role in natural product biosynthesis. In addition, we provide an overview about their genomic and biosynthetic contexts and summarize approaches used to analyze FAAL activity, predict their substrate specificity and to discover new compounds whose biosyntheses involve these enzymes.
{"title":"Fatty acyl-AMP ligases in bacterial natural product biosynthesis","authors":"Anne Liong , Pedro N. Leão","doi":"10.1039/d4np00073k","DOIUrl":"10.1039/d4np00073k","url":null,"abstract":"<div><div>Covering: covering up to 2024</div></div><div><div>Fatty Acyl-AMP Ligases (FAALs) belong to the family of adenylate-forming enzymes and activate fatty acyl substrates through adenylation. FAALs were discovered as key players in various natural product biosynthetic pathways, particularly in the assembly of polyketides and non-ribosomal peptides. These enzymes exhibit a conserved structural architecture that distinguishes them from their close relatives, the Fatty Acyl-CoA Ligases. FAALs display the starter unit in the biosynthesis of diverse natural products where they shuttle fatty acyl substrates into secondary metabolism for further chain elongation and/or modification. In this review, we cover the discovery, distribution and structure of FAALs as well as their role in natural product biosynthesis. In addition, we provide an overview about their genomic and biosynthetic contexts and summarize approaches used to analyze FAAL activity, predict their substrate specificity and to discover new compounds whose biosyntheses involve these enzymes.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 4","pages":"Pages 739-753"},"PeriodicalIF":10.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shuxin Yang , Spencer J. Williams , Myles Courtney , Laura Burchill
Covering: 1960s to 2024
Harmful algal blooms pose a major threat to aquatic ecosystems and can impact human health. The frequency and intensity of these blooms has increased over recent decades, driven primarily by climate change and an increase in nutrient runoff. Algal blooms often produce toxins that contaminate water sources, disrupt fisheries, and harm human health. These blooms may also result in oxygen-deprived environments leading to mass fish deaths that threaten the survival of other aquatic life. In freshwater and estuarine ecosystems, traditional chemical strategies to mitigate algal blooms include the use of herbicides, metal salts, or oxidants. Though effective, these agents are non-selective, toxic to other species, and cause loss of biodiversity. They can persist in ecosystems, contaminating the food web and providing an impetus for cost-effective, targeted algal-control methods that protect ecosystems. In marine ecosystems, harmful algal blooms are even more challenging to treat due to the lack of scalable solutions and the challenge of dispersal of algal control agents in open ocean settings. Natural products derived from algae-bacteria interactions have led to the evolution of diverse bacteria-derived algaecidal natural products, which are highly potent, species specific and have potential for combating harmful algal blooms. They provide valuable starting points for the development of eco-friendly algae control methods. This review provides a comprehensive overview of all bacterial algaecides and their activities, categorized into two major groups: (1) algaecides produced in ecologically significant associations between bacteria and algae, and (2) algaecides with potentially coincidental activity but without an ecological role in specific bacteria–algae interactions. This review contributes to a better understanding of the chemical ecology of parasitic algal–bacterial interactions, “the warfare under the waves”, and highlights the potential applications of bacteria-derived algaecides to provide solutions to harmful algal blooms.
{"title":"Warfare under the waves: a review of bacteria-derived algaecidal natural products†","authors":"Shuxin Yang , Spencer J. Williams , Myles Courtney , Laura Burchill","doi":"10.1039/d4np00038b","DOIUrl":"10.1039/d4np00038b","url":null,"abstract":"<div><div>Covering: 1960s to 2024</div></div><div><div>Harmful algal blooms pose a major threat to aquatic ecosystems and can impact human health. The frequency and intensity of these blooms has increased over recent decades, driven primarily by climate change and an increase in nutrient runoff. Algal blooms often produce toxins that contaminate water sources, disrupt fisheries, and harm human health. These blooms may also result in oxygen-deprived environments leading to mass fish deaths that threaten the survival of other aquatic life. In freshwater and estuarine ecosystems, traditional chemical strategies to mitigate algal blooms include the use of herbicides, metal salts, or oxidants. Though effective, these agents are non-selective, toxic to other species, and cause loss of biodiversity. They can persist in ecosystems, contaminating the food web and providing an impetus for cost-effective, targeted algal-control methods that protect ecosystems. In marine ecosystems, harmful algal blooms are even more challenging to treat due to the lack of scalable solutions and the challenge of dispersal of algal control agents in open ocean settings. Natural products derived from algae-bacteria interactions have led to the evolution of diverse bacteria-derived algaecidal natural products, which are highly potent, species specific and have potential for combating harmful algal blooms. They provide valuable starting points for the development of eco-friendly algae control methods. This review provides a comprehensive overview of all bacterial algaecides and their activities, categorized into two major groups: (1) algaecides produced in ecologically significant associations between bacteria and algae, and (2) algaecides with potentially coincidental activity but without an ecological role in specific bacteria–algae interactions. This review contributes to a better understanding of the chemical ecology of parasitic algal–bacterial interactions, “the warfare under the waves”, and highlights the potential applications of bacteria-derived algaecides to provide solutions to harmful algal blooms.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 4","pages":"Pages 681-719"},"PeriodicalIF":10.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142918711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Correction for ‘Unpacking policy developments in marine natural product research: a scientist's guide to DSI and BBNJ’ by Federica Casolari et al., Nat. Prod. Rep., 2025, 42, 1063–1070, https://doi.org/10.1039/D4NP00070F.
Lipeng Zhou, Xinyu Cai, Ying Wang, Jianbo Yang, Yadan Wang, Jialing Deng, Danni Ye, Lanzhen Zhang, Yue Liu and Shuangcheng Ma
Covering: 2009 up to the end of 2023
Stilbenes, an emblematic group of polyphenols, have attracted the attention of numerous researchers owing to their intriguing polycyclic architectures and diverse bioactivities. In this updated review, natural stilbenes were analysed, especially oligomeric stilbenes, which are an emblematic group of polyphenols that harbor intriguing polycyclic architectures and diverse bioactivities compared with those previously anticipated. Oligomeric stilbenes with unique skeletons comprise a large majority of natural stilbenes owing to their structural changes and different substitutions on the phenyl rings. These compounds can be promising sources of lead compounds for studying new drugs and medicines. In addition, the exploration of unusual structures of oligomeric stilbenes such as polyflavanostilbenes A and B, analysing their absolute stereochemistry, and improving their yield using synthetic biology methods have recently gained interest. This review provides a systematic overview of 409 new stilbenes, which were isolated and identified over time from January 2009 to December 2023, focusing on the classification and biomimetic syntheses of oligomeric stilbenes, in addition to presenting meaningful insights into their structural diversity and biological activities, which will inspire further investigations of biological activities, structure–activity relationships, and screening of drug candidates.
{"title":"Chemistry and biology of natural stilbenes: an update","authors":"Lipeng Zhou, Xinyu Cai, Ying Wang, Jianbo Yang, Yadan Wang, Jialing Deng, Danni Ye, Lanzhen Zhang, Yue Liu and Shuangcheng Ma","doi":"10.1039/D4NP00033A","DOIUrl":"10.1039/D4NP00033A","url":null,"abstract":"<p>Covering: 2009 up to the end of 2023</p><p>Stilbenes, an emblematic group of polyphenols, have attracted the attention of numerous researchers owing to their intriguing polycyclic architectures and diverse bioactivities. In this updated review, natural stilbenes were analysed, especially oligomeric stilbenes, which are an emblematic group of polyphenols that harbor intriguing polycyclic architectures and diverse bioactivities compared with those previously anticipated. Oligomeric stilbenes with unique skeletons comprise a large majority of natural stilbenes owing to their structural changes and different substitutions on the phenyl rings. These compounds can be promising sources of lead compounds for studying new drugs and medicines. In addition, the exploration of unusual structures of oligomeric stilbenes such as polyflavanostilbenes A and B, analysing their absolute stereochemistry, and improving their yield using synthetic biology methods have recently gained interest. This review provides a systematic overview of 409 new stilbenes, which were isolated and identified over time from January 2009 to December 2023, focusing on the classification and biomimetic syntheses of oligomeric stilbenes, in addition to presenting meaningful insights into their structural diversity and biological activities, which will inspire further investigations of biological activities, structure–activity relationships, and screening of drug candidates.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" 2","pages":" 359-405"},"PeriodicalIF":10.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hendrik Luesch, Emma K. Ellis, Qi-Yin Chen and Ranjala Ratnayake
Covering 2010–April 2024
There have been tremendous new discoveries and developments since 2010 in anticancer research based on marine cyanobacteria. Marine cyanobacteria are prolific sources of anticancer natural products, including the tubulin agents dolastatins 10 and 15 which were originally isolated from a mollusk that feeds on cyanobacteria. Decades of research have culminated in the approval of six antibody-drug conjugates (ADCs) and many ongoing clinical trials. Antibody conjugation has been enabling for several natural products, particularly cyanobacterial cytotoxins. Targeting tubulin dynamics has been a major strategy, leading to the discovery of the gatorbulin scaffold, acting on a new pharmacological site. Cyanobacterial compounds with different mechanisms of action (MOA), targeting novel or validated targets in a range of organelles, also show promise as anticancer agents. Important advances include the development of compounds with novel MOA, including apratoxin and coibamide A analogues, modulating cotranslational translocation at the level of Sec61 in the endoplasmic reticulum, largazole and santacruzamate A targeting class I histone deacetylases, and proteasome inhibitors based on carmaphycins, resembling the approved drug carfilzomib. The pipeline extends with SERCA inhibitors, mitochondrial cytotoxins and membrane-targeting agents, which have not yet advanced clinically since the biology is less understood and selectivity concerns remain to be addressed. In addition, efforts have also focused on the identification of chemosensitizing and antimetastatic agents. The review covers the state of current knowledge of marine cyanobacteria as anticancer agents with a focus on the mechanism, target identification and potential for drug development. We highlight the importance of solving the supply problem through chemical synthesis as well as illuminating the biological activity and in-depth mechanistic studies to increase the value of cyanobacterial natural products to catalyze their development.
{"title":"Progress in the discovery and development of anticancer agents from marine cyanobacteria","authors":"Hendrik Luesch, Emma K. Ellis, Qi-Yin Chen and Ranjala Ratnayake","doi":"10.1039/D4NP00019F","DOIUrl":"10.1039/D4NP00019F","url":null,"abstract":"<p>Covering 2010–April 2024</p><p>There have been tremendous new discoveries and developments since 2010 in anticancer research based on marine cyanobacteria. Marine cyanobacteria are prolific sources of anticancer natural products, including the tubulin agents dolastatins 10 and 15 which were originally isolated from a mollusk that feeds on cyanobacteria. Decades of research have culminated in the approval of six antibody-drug conjugates (ADCs) and many ongoing clinical trials. Antibody conjugation has been enabling for several natural products, particularly cyanobacterial cytotoxins. Targeting tubulin dynamics has been a major strategy, leading to the discovery of the gatorbulin scaffold, acting on a new pharmacological site. Cyanobacterial compounds with different mechanisms of action (MOA), targeting novel or validated targets in a range of organelles, also show promise as anticancer agents. Important advances include the development of compounds with novel MOA, including apratoxin and coibamide A analogues, modulating cotranslational translocation at the level of Sec61 in the endoplasmic reticulum, largazole and santacruzamate A targeting class I histone deacetylases, and proteasome inhibitors based on carmaphycins, resembling the approved drug carfilzomib. The pipeline extends with SERCA inhibitors, mitochondrial cytotoxins and membrane-targeting agents, which have not yet advanced clinically since the biology is less understood and selectivity concerns remain to be addressed. In addition, efforts have also focused on the identification of chemosensitizing and antimetastatic agents. The review covers the state of current knowledge of marine cyanobacteria as anticancer agents with a focus on the mechanism, target identification and potential for drug development. We highlight the importance of solving the supply problem through chemical synthesis as well as illuminating the biological activity and in-depth mechanistic studies to increase the value of cyanobacterial natural products to catalyze their development.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" 2","pages":" 208-256"},"PeriodicalIF":10.2,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kevin Mildau, Henry Ehlers, Mara Meisenburg, Elena Del Pup, Robert A. Koetsier, Laura Rosina Torres Ortega, Niek F. de Jonge, Kumar Saurabh Singh, Dora Ferreira, Kgalaletso Othibeng, Fidele Tugizimana, Florian Huber and Justin J. J. van der Hooft
Covering: 2014 to 2023 for metabolomics, 2002 to 2023 for information visualization
LC-MS/MS-based untargeted metabolomics is a rapidly developing research field spawning increasing numbers of computational metabolomics tools assisting researchers with their complex data processing, analysis, and interpretation tasks. In this article, we review the entire untargeted metabolomics workflow from the perspective of information visualization, visual analytics and visual data integration. Data visualization is a crucial step at every stage of the metabolomics workflow, where it provides core components of data inspection, evaluation, and sharing capabilities. However, due to the large number of available data analysis tools and corresponding visualization components, it is hard for both users and developers to get an overview of what is already available and which tools are suitable for their analysis. In addition, there is little cross-pollination between the fields of data visualization and metabolomics, leaving visual tools to be designed in a secondary and mostly ad hoc fashion. With this review, we aim to bridge the gap between the fields of untargeted metabolomics and data visualization. First, we introduce data visualization to the untargeted metabolomics field as a topic worthy of its own dedicated research, and provide a primer on cutting-edge visualization research into data visualization for both researchers as well as developers active in metabolomics. We extend this primer with a discussion of best practices for data visualization as they have emerged from data visualization studies. Second, we provide a practical roadmap to the visual tool landscape and its use within the untargeted metabolomics field. Here, for several computational analysis stages within the untargeted metabolomics workflow, we provide an overview of commonly used visual strategies with practical examples. In this context, we will also outline promising areas for further research and development. We end the review with a set of recommendations for developers and users on how to make the best use of visualizations for more effective and transparent communication of results.
基于lc - ms / ms的非靶向代谢组学是一个快速发展的研究领域，产生了越来越多的计算代谢组学工具，帮助研究人员完成复杂的数据处理、分析和解释任务。在本文中，我们从信息可视化、可视化分析和可视化数据集成的角度回顾了整个非靶向代谢组学工作流程。数据可视化在代谢组学工作流程的每个阶段都是至关重要的一步，它提供了数据检查、评估和共享功能的核心组件。然而，由于有大量可用的数据分析工具和相应的可视化组件，用户和开发人员都很难对已有的可用工具和适合其分析的工具进行概述。此外，数据可视化和代谢组学领域之间几乎没有交叉授粉，使得可视化工具以次要的和主要是临时的方式设计。通过这篇综述，我们旨在弥合非靶向代谢组学和数据可视化领域之间的差距。首先，我们将数据可视化作为一个值得专门研究的主题引入非靶向代谢组学领域，并为研究人员和活跃于代谢组学的开发人员提供数据可视化的前沿可视化研究入门。我们通过讨论从数据可视化研究中出现的数据可视化最佳实践来扩展本入门。其次，我们为可视化工具景观及其在非靶向代谢组学领域的使用提供了一个实用的路线图。在这里，对于非靶向代谢组学工作流程中的几个计算分析阶段，我们通过实际示例概述了常用的视觉策略。在此背景下，我们还将概述有希望进一步研究和发展的领域。最后，我们为开发人员和用户提供了一组关于如何最好地利用可视化来更有效和透明地交流结果的建议。
{"title":"Effective data visualization strategies in untargeted metabolomics†","authors":"Kevin Mildau, Henry Ehlers, Mara Meisenburg, Elena Del Pup, Robert A. Koetsier, Laura Rosina Torres Ortega, Niek F. de Jonge, Kumar Saurabh Singh, Dora Ferreira, Kgalaletso Othibeng, Fidele Tugizimana, Florian Huber and Justin J. J. van der Hooft","doi":"10.1039/D4NP00039K","DOIUrl":"10.1039/D4NP00039K","url":null,"abstract":"<p>Covering: 2014 to 2023 for metabolomics, 2002 to 2023 for information visualization</p><p>LC-MS/MS-based untargeted metabolomics is a rapidly developing research field spawning increasing numbers of computational metabolomics tools assisting researchers with their complex data processing, analysis, and interpretation tasks. In this article, we review the entire untargeted metabolomics workflow from the perspective of information visualization, visual analytics and visual data integration. Data visualization is a crucial step at every stage of the metabolomics workflow, where it provides core components of data inspection, evaluation, and sharing capabilities. However, due to the large number of available data analysis tools and corresponding visualization components, it is hard for both users and developers to get an overview of what is already available and which tools are suitable for their analysis. In addition, there is little cross-pollination between the fields of data visualization and metabolomics, leaving visual tools to be designed in a secondary and mostly <em>ad hoc</em> fashion. With this review, we aim to bridge the gap between the fields of untargeted metabolomics and data visualization. First, we introduce data visualization to the untargeted metabolomics field as a topic worthy of its own dedicated research, and provide a primer on cutting-edge visualization research into data visualization for both researchers as well as developers active in metabolomics. We extend this primer with a discussion of best practices for data visualization as they have emerged from data visualization studies. Second, we provide a practical roadmap to the visual tool landscape and its use within the untargeted metabolomics field. Here, for several computational analysis stages within the untargeted metabolomics workflow, we provide an overview of commonly used visual strategies with practical examples. In this context, we will also outline promising areas for further research and development. We end the review with a set of recommendations for developers and users on how to make the best use of visualizations for more effective and transparent communication of results.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" 6","pages":" 982-1019"},"PeriodicalIF":10.2,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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