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bio-metabolomics-metabolite-annotation
Maintainer FreedomIntelligence · Last updated April 1, 2026
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-metabolite-annotation
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- features <- read.csv('feature_table.csv').
- search_hmdb <- function(mz, adduct = '[M+H]+', ppm = 10) { # Calculate neutral mass from m/z adduct_masses <- list( '[M+H]+' = 1.007276, '[M+Na]+' = 22.989218, '[M-H]-' = -1.007276, '[M+Cl]-' = 34.969402 ).
- neutral_mass <- mz - adduct_masses[[adduct]].
- # Query HMDB (or local database) # Returns putative matches matches <- QueryHMDB(neutral_mass, ppm) return(matches) }.
Source Doc
Excerpt From SKILL.md
Database Matching by m/z
Goal: Generate putative metabolite identifications by matching observed m/z values against HMDB.
Approach: Convert m/z to neutral mass by subtracting adduct mass, then query HMDB within a specified ppm tolerance.
"Annotate my metabolomics features with compound identities" → Match detected features against metabolite databases by exact mass, MS/MS spectra, and retention time to assign compound identities with confidence levels.
library(MetaboAnalystR)
## Apply to all features
annotations <- lapply(features$mz, function(m) search_hmdb(m, '[M+H]+', 10))
MS/MS Spectral Matching
from matchms import calculate_scores
from matchms.importing import load_from_mgf
from matchms.similarity import CosineGreedy
Use cases
- Use when assigning compound identities to detected features in untargeted metabolomics.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- xcms-preprocessing - Generate feature table
- pathway-mapping - Map annotated metabolites to pathways
- proteomics/spectral-libraries - Similar spectral matching concepts
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