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基于质谱的代谢组学中的数据处理与分析。

Data Processing and Analysis in Mass Spectrometry-Based Metabolomics.

机构信息

IMIBIC Mass Spectrometry and Molecular Imaging Unit, Maimonides, Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba (UCO), Córdoba, Spain.

B2SLab, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Barcelona, Spain.

出版信息

Methods Mol Biol. 2023;2571:207-239. doi: 10.1007/978-1-0716-2699-3_20.

DOI:10.1007/978-1-0716-2699-3_20
PMID:36152164
Abstract

Metabolomics is the latest of the omics sciences. It attempts to measure and characterize metabolites-small chemical compounds <1500 Da-on cells, tissue, or biofluids, which are usually products of biological reactions. As metabolic reactions are closer to the phenotype, metabolomics has emerged as an attractive science for various areas of research, including personalized medicine. However, due to the complexity of data obtained and the absence of curated databases for metabolite identification, data processing is the major bottleneck in this area since most technicians lack the required bioinformatics expertise to process datasets in a reliable and fast manner. The aim of this chapter is to describe the available tools for data processing that makes an inexperienced researcher capable of obtaining reliable results without having to undergo through huge parametrization steps.

摘要

代谢组学是组学科学的最新分支。它试图测量和描述代谢物——细胞、组织或生物体液中的小分子化合物(<1500 Da),这些化合物通常是生物反应的产物。由于代谢反应更接近表型,代谢组学已经成为包括个性化医学在内的各个研究领域的热门科学。然而,由于获得的数据的复杂性以及缺乏用于代谢物鉴定的已编目数据库,数据处理是该领域的主要瓶颈,因为大多数技术人员缺乏必要的生物信息学专业知识,无法以可靠和快速的方式处理数据集。本章的目的是描述可用的数据处理工具,使没有经验的研究人员能够获得可靠的结果,而无需经过大量的参数化步骤。

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本文引用的文献

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rMisbeta: A robust missing value imputation approach in transcriptomics and metabolomics data.rMisbeta:转录组学和代谢组学数据中稳健的缺失值插补方法。
Comput Biol Med. 2021 Nov;138:104911. doi: 10.1016/j.compbiomed.2021.104911. Epub 2021 Sep 29.
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mWISE: An Algorithm for Context-Based Annotation of Liquid Chromatography-Mass Spectrometry Features through Diffusion in Graphs.mWISE:通过图中的扩散进行基于上下文的液相色谱-质谱特征注释的算法。
Anal Chem. 2021 Aug 10;93(31):10772-10778. doi: 10.1021/acs.analchem.1c00238. Epub 2021 Jul 28.
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基于 R 的软件工具包用于非靶向代谢组学,膀胱癌生物标志物发现案例研究。
J Proteome Res. 2022 Mar 4;21(3):833-847. doi: 10.1021/acs.jproteome.1c00392. Epub 2021 Jun 23.
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MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights.MetaboAnalyst 5.0:缩小原始光谱与功能见解之间的差距。
Nucleic Acids Res. 2021 Jul 2;49(W1):W388-W396. doi: 10.1093/nar/gkab382.
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Novel Algorithms for Comprehensive Untargeted Detection of Doping Agents in Biological Samples.新型算法可全面、非靶向检测生物样本中的兴奋剂。
Anal Chem. 2021 Jun 1;93(21):7746-7753. doi: 10.1021/acs.analchem.1c01273. Epub 2021 May 21.
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Representing the Metabolome with High Fidelity: Range and Response as Quality Control Factors in LC-MS-Based Global Profiling.高保真度表示代谢组:LC-MS 为基础的全局分析中的范围和响应作为质量控制因素。
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Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.小分子等高线图:定量代谢组学的统一软件包
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Targeted realignment of LC-MS profiles by neighbor-wise compound-specific graphical time warping with misalignment detection.基于邻接法的化合物特异性图形时间扭曲与错配检测实现 LC-MS 图谱的靶向重排。
Bioinformatics. 2020 May 1;36(9):2862-2871. doi: 10.1093/bioinformatics/btaa037.
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CROP: correlation-based reduction of feature multiplicities in untargeted metabolomic data.CROP:无靶向代谢组学数据中基于相关性的特征多重性降低。
Bioinformatics. 2020 May 1;36(9):2941-2942. doi: 10.1093/bioinformatics/btaa012.
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MetumpX-a metabolomics support package for untargeted mass spectrometry.MetumpX-一个用于非靶向质谱的代谢组学支持包。
Bioinformatics. 2020 Mar 1;36(5):1647-1648. doi: 10.1093/bioinformatics/btz765.