使用MAVEN进行液相色谱-质谱数据处理：一种代谢组学分析与可视化引擎
LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine.
作者信息
Clasquin Michelle F, Melamud Eugene, Rabinowitz Joshua D
机构信息
Department of Chemistry and Integrative Genomics, Carl Icahn Laboratory, Princeton, New Jersey, USA.
出版信息
Curr Protoc Bioinformatics. 2012 Mar;Chapter 14:Unit14.11. doi: 10.1002/0471250953.bi1411s37.
Abstract
MAVEN is an open-source software program for interactive processing of LC-MS-based metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple reaction monitoring data or high-resolution full-scan mass spectrometry data. It automatically detects and reports peak intensities for isotope-labeled metabolites. Menu-driven, click-based navigation allows visualization of raw and analyzed data. Here we provide a User Guide for MAVEN. Step-by-step instructions are provided for data import, peak alignment across samples, identification of metabolites that differ strongly between biological conditions, quantitation and visualization of isotope-labeling patterns, and export of tables of metabolite-specific peak intensities. Together, these instructions describe a workflow that allows efficient processing of raw LC-MS data into a form ready for biological analysis.
摘要
MAVEN是一款用于基于液相色谱-质谱联用（LC-MS）的代谢组学数据交互式处理的开源软件程序。MAVEN能够从多反应监测数据或高分辨率全扫描质谱数据中快速且可靠地进行代谢物定量分析。它会自动检测并报告同位素标记代谢物的峰强度。菜单驱动、基于点击的导航方式可实现原始数据和分析后数据的可视化。在此，我们提供MAVEN用户指南。针对数据导入、跨样本峰对齐、鉴定生物条件间差异显著的代谢物、同位素标记模式的定量分析和可视化以及代谢物特异性峰强度表格的导出，我们给出了详细的分步说明。这些说明共同描述了一个工作流程，该流程能将原始LC-MS数据高效处理成可供生物学分析的形式。
相似文献
1
LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine.使用MAVEN进行液相色谱-质谱数据处理：一种代谢组学分析与可视化引擎
Curr Protoc Bioinformatics. 2012 Mar;Chapter 14:Unit14.11. doi: 10.1002/0471250953.bi1411s37.
2
Metabolomic analysis and visualization engine for LC-MS data.LC-MS 数据的代谢组学分析和可视化引擎。
Anal Chem. 2010 Dec 1;82(23):9818-26. doi: 10.1021/ac1021166. Epub 2010 Nov 4.
3
El-MAVEN: A Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics.El-MAVEN：一种用于代谢组学的快速、稳健且用户友好的质谱数据处理引擎。
Methods Mol Biol. 2019;1978:301-321. doi: 10.1007/978-1-4939-9236-2_19.
4
Counting missing values in a metabolite-intensity data set for measuring the analytical performance of a metabolomics platform.计算代谢物强度数据集中的缺失值，以衡量代谢组学平台的分析性能。
Anal Chem. 2015 Jan 20;87(2):1306-13. doi: 10.1021/ac5039994. Epub 2014 Dec 30.
5
ALLocator: an interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis.分配器：一个用于代谢组学液相色谱-电喷雾电离质谱数据集分析的交互式网络平台，支持半自动、用户修订的化合物注释和质量同位素异构体比率分析。
PLoS One. 2014 Nov 26;9(11):e113909. doi: 10.1371/journal.pone.0113909. eCollection 2014.
6
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.Decon2LS：一个用于高分辨率质谱数据自动处理和可视化的开源软件包。
BMC Bioinformatics. 2009 Mar 17;10:87. doi: 10.1186/1471-2105-10-87.
7
Development of chemical isotope labeling liquid chromatography mass spectrometry for silkworm hemolymph metabolomics.开发用于蚕血液代谢组学的化学同位素标记液相色谱-质谱法。
Anal Chim Acta. 2016 Oct 26;942:1-11. doi: 10.1016/j.aca.2016.06.004. Epub 2016 Jun 7.
8
Segment Scan Mass Spectral Acquisition for Increasing the Metabolite Detectability in Chemical Isotope Labeling Liquid Chromatography-Mass Spectrometry Metabolome Analysis.用于提高化学同位素标记液相色谱-质谱代谢组学分析中代谢物可检测性的分段扫描质谱采集
Anal Chem. 2022 Aug 23;94(33):11650-11658. doi: 10.1021/acs.analchem.2c02220. Epub 2022 Aug 4.
9
Development of isotope labeling liquid chromatography mass spectrometry for mouse urine metabolomics: quantitative metabolomic study of transgenic mice related to Alzheimer's disease.用于小鼠尿液代谢组学的同位素标记液相色谱-质谱联用技术的开发：与阿尔茨海默病相关的转基因小鼠的定量代谢组学研究。
J Proteome Res. 2014 Oct 3;13(10):4457-69. doi: 10.1021/pr500828v. Epub 2014 Sep 15.
10
Retention time shift analysis and correction in chemical isotope labeling liquid chromatography/mass spectrometry for metabolome analysis.化学标记液相色谱/质谱代谢组学中保留时间漂移分析与校正。
Rapid Commun Mass Spectrom. 2020 Apr;34 Suppl 1:e8643. doi: 10.1002/rcm.8643. Epub 2020 Feb 8.
引用本文的文献
1
Proximity to a hazardous waste thermal treatment facility alters human physiology: a community-driven pilot study.靠近危险废物热处理设施会改变人体生理机能：一项社区主导的试点研究。
Exp Biol Med (Maywood). 2025 Aug 15;250:10655. doi: 10.3389/ebm.2025.10655. eCollection 2025.
2
Quantitative decoding of coupled carbon and energy metabolism in Pseudomonas putida for lignin carbon utilization.恶臭假单胞菌中木质素碳利用的碳与能量耦合代谢的定量解析
Commun Biol. 2025 Aug 29;8(1):1310. doi: 10.1038/s42003-025-08723-3.
3
The Fanconi Anemia Pathway Inhibits mTOR Signaling and Prevents Accelerated Translation in Head and Neck Cancer Cells.范可尼贫血通路抑制mTOR信号传导并防止头颈癌细胞中的翻译加速。
Cancers (Basel). 2025 Aug 6;17(15):2583. doi: 10.3390/cancers17152583.
4
Classically activated macrophages undergo functionally significant nucleotide metabolism remodelling driven by nitric oxide.经典激活的巨噬细胞经历由一氧化氮驱动的具有功能意义的核苷酸代谢重塑。
Nat Metab. 2025 Aug 4. doi: 10.1038/s42255-025-01337-3.
5
Gut microbiota-derived metabolite trimethylamine N-oxide alters the host epigenome through inhibition of S-adenosylhomocysteine hydrolase.肠道微生物群衍生的代谢产物氧化三甲胺通过抑制S-腺苷同型半胱氨酸水解酶改变宿主表观基因组。
J Biol Chem. 2025 Jul 25;301(9):110521. doi: 10.1016/j.jbc.2025.110521.
6
Respiratory Syncytial Virus Elicits Glycolytic Metabolism in Pediatric Upper and Lower Airways.呼吸道合胞病毒引发小儿上、下呼吸道的糖酵解代谢。
Viruses. 2025 May 14;17(5):703. doi: 10.3390/v17050703.
7
Mass-spectrometry based metabolomics: an overview of workflows, strategies, data analysis and applications.基于质谱的代谢组学：工作流程、策略、数据分析及应用概述
Proteome Sci. 2025 May 26;23(1):5. doi: 10.1186/s12953-025-00241-8.
8
A shared alarmone-GTP switch controls persister formation in bacteria.一种共享的警报素-GTP开关控制细菌中持留菌的形成。
Nat Microbiol. 2025 May 15. doi: 10.1038/s41564-025-02015-6.
9
Specific Bacterial Taxa and Their Metabolite, DHPS, May Be Linked to Gut Dyshomeostasis in Patients with Alzheimer's Disease, Parkinson's Disease, and Amyotrophic Lateral Sclerosis.特定细菌分类群及其代谢产物二氢蝶酸合酶（DHPS）可能与阿尔茨海默病、帕金森病和肌萎缩侧索硬化症患者的肠道生态失调有关。
Nutrients. 2025 May 6;17(9):1597. doi: 10.3390/nu17091597.
10
N-terminomics and proteomics analysis of Calpain-2 reveal key proteolytic processing of metabolic and cell adhesion proteins.钙蛋白酶-2的N端蛋白质组学和蛋白质组学分析揭示了代谢和细胞粘附蛋白的关键蛋白水解过程。
Protein Sci. 2025 May;34(5):e70144. doi: 10.1002/pro.70144.
本文引用的文献
1
Riboneogenesis in yeast.酵母中的核糖生成。
Cell. 2011 Jun 10;145(6):969-80. doi: 10.1016/j.cell.2011.05.022.
2
Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli.大规模 13C 通量分析揭示了大肠杆菌呼吸和发酵代谢的转录控制明显不同。
Mol Syst Biol. 2011 Mar 29;7:477. doi: 10.1038/msb.2011.9.
3
Metabolomics and its practical value in pharmaceutical industry.代谢组学及其在制药行业的实际价值。
Curr Drug Metab. 2011 May;12(4):345-58. doi: 10.2174/138920011795202947.
4
Metabolomic analysis and visualization engine for LC-MS data.LC-MS 数据的代谢组学分析和可视化引擎。
Anal Chem. 2010 Dec 1;82(23):9818-26. doi: 10.1021/ac1021166. Epub 2010 Nov 4.
5
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.MZmine 2：用于处理、可视化和分析基于质谱的分子图谱数据的模块化框架。
BMC Bioinformatics. 2010 Jul 23;11:395. doi: 10.1186/1471-2105-11-395.
6
Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer.反相离子对液相色谱-独立轨道阱质谱联用进行代谢组学分析。
Anal Chem. 2010 Apr 15;82(8):3212-21. doi: 10.1021/ac902837x.
7
Bacterial adaptation through distributed sensing of metabolic fluxes.细菌通过代谢通量的分布式感知进行适应性进化。
Mol Syst Biol. 2010;6:355. doi: 10.1038/msb.2010.10. Epub 2010 Mar 9.
8
A guided tour of the Trans-Proteomic Pipeline.《跨蛋白质组学分析流程指南》
Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375.
9
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate.癌症相关的 IDH1 突变会产生 2-羟基戊二酸。
Nature. 2009 Dec 10;462(7274):739-44. doi: 10.1038/nature08617.
10
Metabolic systems biology.代谢系统生物学。
FEBS Lett. 2009 Dec 17;583(24):3900-4. doi: 10.1016/j.febslet.2009.09.031.
Zotero 插件