HolobiomicsLab MASST Repository-Scale Spectral Search (Reverse Metabolomics)
Summary
End-to-end reverse metabolomics: take one molecule and find its public-dataset footprint with MASST, then add ecological context and co-occurrence interpretation.
When to use
Use when you have a spectrum or feature of interest and want to know where else it occurs across all public metabolomics data — query preparation, repository-scale fastMASST search, specialized microbe/plant/food MASST for ecological context, and co-occurrence analysis.
When NOT to use
- The data is not LC-MS.
- You need a single atomic step, not the full pipeline (use the leaf skill directly via the router).
Stages
Stage 1 — spectrum_prep
Goal: prepare a query MS/MS spectrum / USI for search
EDAM operation: operation_3215
Inputs: mgf · Outputs: tsv
Candidate leaf skills: usi-spectrum-retrieval-and-loading (primary), spectral-data-loading-from-repository, usi-namespace-parsing, usi-string-parsing-and-resolution, usi-spectrum-identifier-encoding
Tools (primary): spectrum_utils, Python, matplotlib, GNPS public library, ProteomeXchange (PXD datasets)
Other candidate tools: NumPy, GNPS Molecular Networking, MassBank, MetaboLights, Metabolomics Workbench, MS2LDA, GNPS Spectral Libraries, ProteoXchange Repository, QR Code Generation Library, USI Resolver and Displayer
Grounding: 2 KB(s); DOIs: 10.1021/acs.analchem.9b04884, 10.1101/2020.05.09.086066
Stage 2 — masst_search
Goal: repository-scale spectral search (fastMASST)
EDAM operation: operation_3631
Inputs: tsv · Outputs: tsv
Candidate leaf skills: spectral-database-query-execution (primary), spectral-match-result-consolidation, mass-spectrometry-database-search, mass-spectrometry-reference-database-integration, spectral-match-interpretation
Tools (primary): MASST, GNPS, MASST+, CLUSTERING+, PAIRING+
Other candidate tools: metadataMASST, microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST, Fast Search API, GNPS_MASST, GNPS Molecular Networking, MZmine
Grounding: 3 KB(s); DOIs: 10.1038/s41538-022-00137-3, 10.1038/s41564-023-01575-9, 10.1038/s41587-023-01985-4
Stage 3 — specialized_masst [OPTIONAL]
Goal: (optional) ecological context via microbe/plant/food MASST
EDAM operation: operation_3631
Inputs: tsv · Outputs: tsv
Candidate leaf skills: domain-specific-spectrum-search-implementation (primary), masst-output-visualization, multi-domain-search-result-aggregation, metadata-harmonization-across-sources
Tools (primary): microbeMASST, metadataMASST, GNPS_MASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST, Fast Search API, MZmine
Grounding: 2 KB(s); DOIs: 10.1038/s41538-022-00137-3, 10.1038/s41564-023-01575-9
Stage 4 — cooccurrence
Goal: co-occurrence / reverse-metabolomics interpretation
EDAM operation: operation_3659
Inputs: tsv · Outputs: tsv
Candidate leaf skills: metabolite-metadata-integration (primary), sample-centric-metabolite-annotation, tandem-mass-spectrometry-metadata-standardization, ms-ms-spectral-library-matching, compound-database-matching
Tools (primary): msFeaST, pandas, jupyter-notebook
Other candidate tools: ENPKG, MZmine, enpkg_mn_isdb_taxo, enpkg_sirius_canopus, enpkg_meta_analysis, SIRIUS, Open Tree of Life, Wikidata, NPClassifier, ChEMBL, matchms, pubchempy, RDKit, Python, masscube, TandemMatch, Mirador, PeakQC, Spectra, MetFrag, R, PubChem, COCONUT
Grounding: 6 KB(s); DOIs: 10.1021/acscentsci.3c00800, 10.1021/jasms.4c00146, 10.1038/s41467-025-60640-5, 10.1093/bioinformatics/btae584 …
Grounding
Each stage carries the kb_slugs/dois of the leaves it draws on. Ground any stage against its source paper with the collection's /ground command or bin/perspicacite_kb_bind.py (Perspicacité KB; serverless local-clone fallback).
Verification contract
workflow.yaml is gradable by asb solve-workflow (checkpoint mode). Each stage declares typed outputs; the final stage emits the master deliverable.
Provenance
Generated by compose_workflows.py (semantic binding + EDAM-aware primary selection). derived_from_workflows lists ASB per-paper workflows whose structure corroborated this pipeline — the eval-ablation set (SPEC §8). Staging only; promote via release_gate.py.