Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

被引:529
作者
Blazenovic, Ivana [1 ]
Kind, Tobias [1 ]
Ji, Jian [2 ]
Fiehn, Oliver [1 ,3 ]
机构
[1] Univ Calif Davis, NIH West Coast Metabol Ctr, UC Davis Genome Ctr, Davis, CA 95616 USA
[2] Jiangnan Univ, State Key Lab Food Sci & Technol, Sch Food Sci, Synerget Innovat Ctr Food Safety & Nutr, Wuxi 214122, Peoples R China
[3] King Abdulaziz Univ, Dept Biochem, Fac Sci, Jeddah 21589, Saudi Arabia
基金
美国国家卫生研究院; 美国国家科学基金会;
关键词
tandem mass spectrometry; library search; in silico fragmentation; high resolution mass spectrometry; compound identification; metabolomics; COLLISION CROSS-SECTION; MOBILITY-MASS-SPECTROMETRY; RETENTION TIME PREDICTION; MOLECULAR-STRUCTURE DATABASES; 1ST PRINCIPLES CALCULATION; ION MOBILITY; METABOLITE IDENTIFICATION; NATURAL-PRODUCTS; LIQUID-CHROMATOGRAPHY; GLOBAL METABOLOMICS;
D O I
10.3390/metabo8020031
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.
引用
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页数:23
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