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Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools
BackgroundUntargeted metabolomics approaches based on mass spectrometry obtain comprehensive profiles of complex biological samples. However, on...
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Metabolite discovery through global annotation of untargeted metabolomics data
Liquid chromatography–high-resolution mass spectrometry (LC-MS)-based metabolomics aims to identify and quantify all metabolites, but most LC-MS...
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Functional annotation and importance of marine bacterial transporters of plankton exometabolites
Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of...
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GMMAD: a comprehensive database of human gut microbial metabolite associations with diseases
BackgroundThe natural products, metabolites, of gut microbes are crucial effect factors on diseases. Comprehensive identification and annotation of...
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Predicting intercellular communication based on metabolite-related ligand-receptor interactions with MRCLinkdb
BackgroundMetabolite-associated cell communications play critical roles in maintaining human biological function. However, most existing tools and...
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PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management
IntroductionAccuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However,...
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Databases and Tools to Investigate Protein-Metabolite Interactions
Protein-metabolite interactions (PMIs) are directly responsible for the regulation of numerous processes. From the direct regulation of enzymes to...
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NMRFinder: a novel method for 1D 1H-NMR metabolite annotation
IntroductionMethods for the automated and accurate identification of metabolites in 1D 1 H-NMR samples are crucial, but this is still an unsolved...
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MetFID: artificial neural network-based compound fingerprint prediction for metabolite annotation
IntroductionMetabolite annotation is a critical and challenging step in mass spectrometry-based metabolomic profiling. In a typical untargeted...
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Limited Proteolysis–Mass Spectrometry to Identify Metabolite–Protein Interactions
Metabolite–protein interactions regulate diverse cellular processes, prompting the development of methods to investigate the metabolite–protein...
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Metabolite-Based Genome-Wide Association Studies of Large-Scale Metabolome Analysis to Illustrate Alterations in the Metabolite Landscape of Plants upon Responses to Stresses
Given that anthropogenic activities are evoking a profound effect on the climate resulting in more extreme events such as severe drought and heat...
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Problems, principles and progress in computational annotation of NMR metabolomics data
BackgroundCompound identification remains a critical bottleneck in the process of exploiting Nuclear Magnetic Resonance (NMR) metabolomics data,...
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Assembly, Annotation and Visualization of NGS Data
The next-generation sequencing technologies have revolutionized the field of agriculture with the advent of ever-evolving chemistries and a reduction...
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LiLA: lipid lung-based ATLAS built through a comprehensive workflow designed for an accurate lipid annotation
Accurate lipid annotation is crucial for understanding the role of lipids in health and disease and identifying therapeutic targets. However,...
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De novo genome assembly and annotation of the medicinal plant Tinospora cordifolia (Willd.) Miers ex Hook. f. & Thom’s
Indian natural climbing shrub Tinospora cordifolia , often known as “Guduchi” and “Amrita,” is a highly esteemed medicinal plant in the Indian system...
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Reproducible mass spectrometry data processing and compound annotation in MZmine 3
Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to investigate manually. For...
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Identification of Plant Protein–Metabolite Interactions by Limited Proteolysis-Coupled Mass Spectrometry (LiP-MS)
The interactions between metabolites and proteins constitute crucial events in cell signaling and metabolism. In recent years, large-scale proteomics...
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Advanced high-resolution chromatographic strategies for efficient isolation of natural products from complex biological matrices: from metabolite profiling to pure chemical entities
The isolation of pure compounds from extracts represents a key step common to all investigations of natural product (NP) research. Isolation methods...
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Tissue- and time-dependent metabolite profiles during early grain development under normal and high night-time temperature conditions
BackgroundWheat grain development in the first few days after pollination determines the number of endosperm cells that influence grain yield...
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The Y-ome Conundrum: Insights into Uncharacterized Genes and Approaches for Functional Annotation
The ever-increasing availability of genome sequencing data has revealed a substantial number of uncharacterized genes without known functions across...
