Resources

Introduction to NMR-based metabolomics and sample preparation for NMR

A virtual NMR-based metabolomics training by MSA, UNISA, and DIPLOMICS which includes a detailed tutorial on sample preparation for NMR analysis. It emphasises minimal sample handling, proper extraction techniques, and preparation protocols to ensure accurate metabolite profiling, highlighting NMR’s non-destructive nature and reliability in plant metabolomics studies.

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A Basic Metabolomics Strategy for Statistical Analysis and Metabolite Annotation

This video focuses on statistical analysis and metabolite annotation in metabolomics. Learn to identify significant metabolites using multivariate and univariate statistical methods, then annotate compounds by matching spectral data with reference databases. The video highlights essential tools and resources for transforming raw data into biologically meaningful results for biomarker discovery.

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MS-DIAL5 tutorial

This MS-DIAL5 tutorial covers streamlined workflows for untargeted metabolomics, lipidomics, and proteomics analysis. The latest version features an improved graphical interface and eliminates the need for converting vendor-specific raw data into ABF format, allowing direct import from multiple instrument types, making data processing faster and more user-friendly for researchers.

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GNPS2 Documentation

GNPS2 Documentation guides users through this web-based mass spectrometry platform developed by UC Riverside’s Wang Lab. It covers tools and workflows for identifying and discovering new molecules in small molecule and natural products’ data. The documentation includes quick-start guides, detailed tutorials, analysis workflows, and community resources for collaborative mass spectrometry research and data sharing.

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Human Metabolome Database (HMDB)

HMDB is a comprehensive free database featuring 220,945 human metabolites and 8,610 linked proteins. Each entry includes 130 data fields covering chemical, clinical, and biochemical information, with connections to major databases like KEGG, PubChem, and UniProt. It supports metabolomics, biomarker discovery, and clinical chemistry through advanced text, spectral, and structural searches. The platform includes DrugBank, T3DB, SMPDB, and FooDB, encompassing drugs, toxins, pathways, and food components for extensive biomedical research applications.

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Kyoto Encyclopedia of Genes and Genomes (KEGG)

KEGG is a user-friendly database helping scientists understand biological systems in humans, plants, and other organisms. It organises molecular information from DNA sequencing into easy-to-navigate formats. Users can search for genes, proteins, metabolic pathways, chemical compounds, diseases, and drug interactions. Think of it as a digital library connecting biological processes, showing how cells process nutrients and medicines. KEGG is essential for metabolomics researchers exploring how living organisms function at the molecular level.

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PubChem

PubChem is a free NCBI database offering extensive chemical information crucial for metabolomics. It provides compound structures, physicochemical properties, biological activities, and links to pathways and bioassays. Researchers can identify metabolites, explore chemical interactions, and integrate data with omics studies. PubChem supports structure-based searches, annotation of metabolite profiles, and cross-referencing with KEGG, HMDB, and other resources, making it a key tool for biomarker discovery and systems biology.

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MassBank

MassBank is a free, open-access database storing mass spectral data from small chemical compounds, including metabolites, drugs, and environmental substances. Scientists use it to identify unknown compounds by comparing their experimental spectra with MassBank’s reference library. The database contains thousands of high-quality mass spectra collected from research groups worldwide. Users can search by chemical structure, compound name, or spectral patterns, making it an essential tool for metabolomics researchers identifying molecules in biological samples.

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MetaboAnalyst

MetaboAnalyst is a free web-based platform for analysing metabolomics data. It helps researchers process raw experimental data, identify significant metabolites, and interpret biological meanings through statistical analysis and pathway mapping. Users can upload various data types, including mass spectrometry peaks and compound concentrations. The platform supports end-to-end analysis from spectra processing to functional interpretation, making complex metabolomics analysis accessible without requiring expensive software or advanced programming skills. It’s ideal for biomarker discovery and disease research.

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Global Natural Products Social Molecular Networking (GNPS)

GNPS is a free web-based platform for sharing and analysing mass spectrometry data. It helps researchers identify unknown compounds by comparing their experimental spectra with community-contributed reference libraries. The platform enables continuous automatic reanalysis of deposited data, creating connections between researchers studying similar molecules. Users can perform molecular networking to visualise chemical relationships, search public datasets, and contribute their own spectral data to benefit the global scientific community.

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MS-DIAL

MS-DIAL is free, open-source software for analyzing metabolomics and lipidomics data. It works with various mass spectrometry instruments from multiple manufacturers, handling the complete data processing workflow from raw data import to statistical analysis. The software features spectral deconvolution and includes built-in reference libraries, helping researchers identify metabolites and lipids without requiring expensive commercial software. Its user-friendly interface makes complex mass spectrometry data analysis accessible for beginners in metabolomics.

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MZmine

MZmine is a free, open-source software for processing mass spectrometry data in metabolomics and lipidomics research. It supports multiple data formats from various instrument vendors and handles LC-MS, GC-MS, MS-imaging, and ion mobility data. The software provides complete workflows from raw data import through feature detection, compound identification, and statistical analysis. MZmine integrates with popular tools like GNPS, SIRIUS, and MetaboAnalyst, making comprehensive metabolomics analysis accessible for researchers without requiring programming skills.

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