LC-MS (liquid chromatography–mass spectrometry) has become an essential analytical technology for natural product research, metabolomics, and herbal medicine quality control. By combining high-resolution mass spectrometry with advanced data analysis workflows, LC-MS enables researchers to perform compound identification, MS/MS annotation, and comprehensive chemical profiling of complex biological samples.
This resource provides practical guides, software recommendations, databases, and workflow strategies for LC-MS data processing, molecular networking, and natural product identification. It covers commonly used LC-MS metabolomics tools, including SIRIUS, GNPS, MS-DIAL, and MZmine, to help researchers improve data interpretation and accelerate natural product discovery.
Featured LC-MS Tools
SIRIUS
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SIRIUS is a computational platform for molecular formula prediction, structure annotation, and MS/MS-based compound identification in high-resolution mass spectrometry workflows.
Key applications:
- Molecular formula prediction
- Structure annotation
- MS/MS interpretation
- Natural product research workflows
GNPS (Global Natural Products Social Molecular Networking)
GNPS (Global Natural Products Social Molecular Networking) is a web-based platform designed for mass spectrometry data analysis, molecular networking, and natural product discovery.
By connecting MS/MS spectra through spectral similarity, GNPS enables researchers to visualize chemical relationships, annotate metabolites, and explore complex natural product chemical space. It is widely used in metabolomics, dereplication, and large-scale LC-MS/MS studies.
Key applications:
- Molecular networking
- MS/MS spectral library matching
- Natural product dereplication
- Metabolomics data analysis
- Chemical relationship visualization
MS-DIAL
MS-DIAL is an open-source comprehensive software platform for processing and interpreting untargeted metabolomics data from LC-MS and GC-MS experiments.
The software provides an integrated workflow including peak detection, alignment, deconvolution, metabolite annotation, and visualization. MS-DIAL supports multiple mass spectrometry platforms and is widely used for metabolomics and natural product analysis.
Key applications:
- LC-MS metabolomics data processing
- Peak detection and alignment
- MS/MS spectrum deconvolution
- Metabolite annotation
- Untargeted metabolomics workflows
MZmine
MZmine is an open-source framework for processing, visualization, and analysis of mass spectrometry data, particularly for LC-MS-based metabolomics research.
It provides flexible workflows for raw data processing, including feature detection, chromatographic alignment, isotope grouping, and statistical analysis. MZmine is commonly used by researchers who need customizable LC-MS data processing pipelines.
Key applications:
- LC-MS feature detection
- Chromatographic alignment
- Data preprocessing
- Visualization of metabolomics datasets
- Custom LC-MS workflow development
Choosing the Right LC-MS Tool
Different LC-MS research questions require different analytical approaches.
For compound annotation and molecular formula prediction:
→ SIRIUS
For molecular networking and spectral exploration:
→ GNPS
For untargeted metabolomics data processing:
→ MS-DIAL
For flexible LC-MS feature processing workflows:
→ MZmine