WTV2.0:具有综合选择性离子监测采集模式的高覆盖率植物挥发物组学方法。

IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Plant Pub Date : 2024-06-03 Epub Date: 2024-04-29 DOI:10.1016/j.molp.2024.04.012
Honglun Yuan, Yiding Jiangfang, Zhenhuan Liu, Rongxiu Su, Qiao Li, Chuanying Fang, Sishu Huang, Xianqing Liu, Alisdair R Fernie, Jie Luo
{"title":"WTV2.0:具有综合选择性离子监测采集模式的高覆盖率植物挥发物组学方法。","authors":"Honglun Yuan, Yiding Jiangfang, Zhenhuan Liu, Rongxiu Su, Qiao Li, Chuanying Fang, Sishu Huang, Xianqing Liu, Alisdair R Fernie, Jie Luo","doi":"10.1016/j.molp.2024.04.012","DOIUrl":null,"url":null,"abstract":"<p><p>Volatilomics is essential for understanding the biological functions and fragrance contributions of plant volatiles. However, the annotation coverage achieved using current untargeted and widely targeted volatomics (WTV) methods has been limited by low sensitivity and/or low acquisition coverage. Here, we introduce WTV 2.0, which enabled the construction of a high-coverage library containing 2111 plant volatiles, and report the development of a comprehensive selective ion monitoring (cSIM) acquisition method, including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method, that can acquire the smallest but sufficient number of ions for most plant volatiles, as well as the automatic qualitative and semi-quantitative analysis of cSIM data. Importantly, the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library, utilizing the obtained cSIM data. We showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method, doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit, and led to the discovery of menthofuran as a novel flavor compound in passion fruit. WTV 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":null,"pages":null},"PeriodicalIF":17.1000,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"WTV2.0: A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode.\",\"authors\":\"Honglun Yuan, Yiding Jiangfang, Zhenhuan Liu, Rongxiu Su, Qiao Li, Chuanying Fang, Sishu Huang, Xianqing Liu, Alisdair R Fernie, Jie Luo\",\"doi\":\"10.1016/j.molp.2024.04.012\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Volatilomics is essential for understanding the biological functions and fragrance contributions of plant volatiles. However, the annotation coverage achieved using current untargeted and widely targeted volatomics (WTV) methods has been limited by low sensitivity and/or low acquisition coverage. Here, we introduce WTV 2.0, which enabled the construction of a high-coverage library containing 2111 plant volatiles, and report the development of a comprehensive selective ion monitoring (cSIM) acquisition method, including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method, that can acquire the smallest but sufficient number of ions for most plant volatiles, as well as the automatic qualitative and semi-quantitative analysis of cSIM data. Importantly, the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library, utilizing the obtained cSIM data. We showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method, doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit, and led to the discovery of menthofuran as a novel flavor compound in passion fruit. WTV 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.</p>\",\"PeriodicalId\":19012,\"journal\":{\"name\":\"Molecular Plant\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":17.1000,\"publicationDate\":\"2024-06-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular Plant\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1016/j.molp.2024.04.012\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/4/29 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Plant","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1016/j.molp.2024.04.012","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/4/29 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

挥发性物质组学对于了解植物挥发性物质的生物功能和香味贡献至关重要。然而,由于灵敏度低和/或采集覆盖率低,目前非靶向和广泛靶向方法的注释覆盖范围受到了限制。在此,我们介绍 WTV 2.0。它可以构建一个包含 2111 种植物挥发物的高覆盖率库;开发一种综合选择离子监测(cSIM)采集方法,该方法包含了大多数植物挥发物所需的最少但足够的离子,包括为每种化合物选择离子数最少的特征定性离子,以及采集方法的优化分段;最后,对 cSIM 数据进行自动定性和半定量分析。此外,利用所获得的 cSIM 数据,还可以通过加入化合物库中不存在的化合物来自我扩展化合物库和采集方法。与无目标方法相比,WTV 2.0 将信噪比中值提高了 7.6 倍,与无目标方法和 WTV 1.0 方法相比,番茄果实中的注释覆盖率提高了一倍,并发现了百香果中的新型风味化合物薄荷呋喃。WTV 2.0 是一个 Python 库,具有友好的用户界面,适用于任何物种的挥发性物质和初级代谢物分析。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
WTV2.0: A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode.

Volatilomics is essential for understanding the biological functions and fragrance contributions of plant volatiles. However, the annotation coverage achieved using current untargeted and widely targeted volatomics (WTV) methods has been limited by low sensitivity and/or low acquisition coverage. Here, we introduce WTV 2.0, which enabled the construction of a high-coverage library containing 2111 plant volatiles, and report the development of a comprehensive selective ion monitoring (cSIM) acquisition method, including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method, that can acquire the smallest but sufficient number of ions for most plant volatiles, as well as the automatic qualitative and semi-quantitative analysis of cSIM data. Importantly, the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library, utilizing the obtained cSIM data. We showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method, doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit, and led to the discovery of menthofuran as a novel flavor compound in passion fruit. WTV 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Molecular Plant
Molecular Plant 植物科学-生化与分子生物学
CiteScore
37.60
自引率
2.20%
发文量
1784
审稿时长
1 months
期刊介绍: Molecular Plant is dedicated to serving the plant science community by publishing novel and exciting findings with high significance in plant biology. The journal focuses broadly on cellular biology, physiology, biochemistry, molecular biology, genetics, development, plant-microbe interaction, genomics, bioinformatics, and molecular evolution. Molecular Plant publishes original research articles, reviews, Correspondence, and Spotlights on the most important developments in plant biology.
期刊最新文献
Architecture of the ATP-driven motor for protein import into chloroplasts. Mirids secrete a TOPLESS targeting protein to enhance JA-mediated defense and gossypol accumulation for antagonizing cotton bollworms on cotton plants. On the evolution and genetic diversity of the bread wheat D genome. Sucrose-responsive osmoregulation of plant cell size by a long non-coding RNA. The metal tolerance protein OsMTP11 facilitates cadmium sequestration in the vacuoles of leaf vascular cells for restricting its translocation into rice grains.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1