What does this strategy enable?
MS2LDA links spectra through learned Mass2Motifs, including molecules without high overall spectral similarity.
Transferable workflow
Workflow
- 1
Prepare precursor-linked spectra
The original workflow uses XCMS, MzMatch and RMassBank to prepare fragment and loss features.
- 2
- 3
Interpret and inspect assignments
Compare motif patterns with reference spectra and chemical knowledge; examine associated precursors.
Connected resources
Tools used in this strategy
Evidence of reuse
Published implementations and adaptations
These papers applied, adapted, extended, benchmarked or formalized the Strategy after its originating publication. They are examples of precedent, not a ranking of software choices.
Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics
MS2LDA+ learns shared motifs across samples while retaining sample-specific prevalence for comparison.
Navigator tools used: MS2LDA
Strategy profile
Related objectives
Molecular-family discovery
Components
Preprocessing and feature extraction, Annotation or identification, Spectral search
Scope and considerations
Designed for
- Substructure hypotheses from collections of MS/MS spectra.
Important requirements
- Precursor-linked fragmentation spectra and consistent fragment/loss representation.
Considerations
- A motif need not identify a unique substructure or complete molecule. Expert interpretation remains necessary.
Reusable resources
Publication
Topic modeling for untargeted substructure exploration in metabolomics